Single-molecule detection system and methods

ABSTRACT

Embodiments encompass a single-molecule detection system and methods of using the detection system to detect an object. Further, embodiments encompass a detection system comprising a movable light coupler, a waveguide, and a light detector. Embodiments further encompass methods of single-molecule detection, including methods of single-molecule nucleic acid sequencing.

PRIORITY INFORMATION

This application claims priority to U.S. application Ser. No.61/314,037, filed Mar. 15, 2010, which is incorporated herein byreference in its entirety.

TECHNICAL FIELD

The application relates to a single-molecule detection system andmethods of using the detection system to detect an object. Further, theapplication relates to a detection system comprising a movable lightcoupler, a waveguide, and a light detector. The application also relatesto methods of loading samples to a single-molecule detection system. Theapplication further relates to methods of single-molecule detection,including methods of single-molecule nucleic acid sequencing.

BACKGROUND

Most conventional chemical or biochemical assays are based on “bulk”measurements. In such measurements, a collective behavior of a pluralityof molecules within a certain volume of a sample solution is measured todetermine the properties of the molecules. However, in many situations,bulk measurement approaches cannot be utilized, such as when samplevolume is too small or the concentration of a target molecule is too lowfor a given technique's limit of sensitivity in detecting targetmolecules. In recent years, the detection of single molecules has becomepossible. Single-molecule detection offers much higher sensitivity andprovides more detailed information than conventional bulk measurements.The development of single-molecule instrument sensitivity also promisesnew opportunities for high-sensitivity biological molecule detection anddiagnosis, as described in Qiu, H., et al., “Fluorescencesingle-molecule counting assays for high-sensitivity detection ofcytokines and chemokines”, CLINICAL CHEMISTRY 53(11):2010-2012 (2007).

A description of approaches for achieving single-molecule detection isprovided in Moerner, W. E. and Fromm, D. P., “REVIEW ARTICLE: Methods ofsingle-molecule fluorescence spectroscopy and microscopy”, REVIEW OFSCIENTIFIC INSTRUMENTS 74(8): 3597-3619 (2003) and in Walter, N. G., etal., “Do-it-yourself guide: how to use the modern single-moleculetoolkit”, NATURE METHODS 5:475-489 (2008). These reviews also discussmethods and apparatuses known in the art that have been used or proposedfor single-molecule detection. Applications of single-molecule detectioninclude single-molecule DNA sequencing, single-molecule biomarkerdetection and miniaturized flow-cytometry-like detection.

Optimized systems and methods for single molecule detection have greatpotential for accelerating DNA sequencing technology. The Human GenomeProject (HGP) spurred a great increase in DNA sequencing throughput.This increase, along with technical improvements, resulted in acorresponding drop in sequencing costs. While the first genome required13 years and nearly three billion US dollars to completely sequence, ithas been predicted that DNA sequencing technologies may ultimatelybecome sufficiently affordable for personal genomics to be an integralcomponent of routine clinical care (McGuire et al., SCIENCE 317:1687(2007)). Personal genomes represent a paradigm shift in medicaltreatment for both patients and health care providers. By managinggenetic risk factors for disease, health care providers can more readilypractice preventative medicine and provide customized treatment. Withlarge banks of completed genomes, drug design and administration can bemore efficient, thereby accelerating the nascent field ofpharmacogenomics. However, this acceleration will depend on therealization of robust, high-throughput, and low-cost DNA sequencingtechnologies.

To achieve single-molecule detection, an optical system must be able toselectively excite the molecule of interest in a complicatedenvironment, and be able to avoid the interference from the backgroundnoise and detect the weak light emitted from that single molecule. Oneof the approaches for achieving single-molecule detection is locatingthe molecule of interest inside a confined space facilitating detectionof light emitted from one molecule. U.S. Pat. No. 6,917,726 discloses amicroscopy system incorporating a zero-mode waveguide (ZMW), which canfacilitate the detection of single molecules by using nano-scale wellsin which defined excitation light fields are created. Placement ofmolecules within these nanowells, and thus within these definedexcitation light fields, greatly minimizes noise, thereby enhancing thedetectability of light emitted from a single molecule. See also, forexample, U.S. Pat. No. 6,917,726; U.S. Pat. No. 7,170,050; and U.S. Pat.No. 7,486,865. However, loading of the single-molecule sample into theexcitation field requires attachment of the molecules to the bottom ofthe ZMW in the nanowells, which is difficult and inefficient (Eid etal., SCIENCE, 323:133-138 (2009)). Only wells containing onesingle-molecule sample are useful, while empty wells or wells containingmultiple single-molecule samples are not.

Improved methods of sample loading with higher success rates aredisclosed in U.S. patent publication no. 2010/0009872. These methodsutilize a nano-scale particle to carry a single-molecule sample to thetop opening of the nanowell and deliver the sample to the bottom of thewell, where the sample may be exposed to the excitation field. However,the process involves many steps and chemical reactions to transfer thesingle-molecule sample from the nanoparticle carrier to the bottom ofthe well. Furthermore, the loaded wells are either impossible ordifficult to reuse.

International Patent Publication Number WO 2009/017678 disclosed methodsof single-molecule nucleic acid sequencing in which a single polymeraseis immobilized on a surface to repeatedly sequence a circular nucleicacid template, thereby improving the accuracy of single-moleculesequencing. In this method for optical detection of single-moleculesequencing, immobilization of reactants directly on the surface confinedreactions to within a zeptoliter volume. However, the difficulty ofbinding a single molecule of an enzyme or a nucleic acid onto thesurface limits high-throughput use. Furthermore, a sequencing reactionin which a polymerase is immobilized directly on the surface will beterminated whenever the polymerase loses its activity, preventingcompletion of sequencing analysis at that site. In order to immobilize amolecule or enzyme in place, as set forth in WO 2009/017678, the regionof surface must be well-defined and the chemical property of that regionmust be precisely controlled. This presents difficulties and added costsfor device manufacturing.

Therefore, there is a need for improved systems and methods fordetection of single-molecule objects.

SUMMARY OF CERTAIN EMBODIMENTS

There is provided a system for detecting an object, such as asingle-molecule object, wherein the detection system comprises a movablelight coupler, a light detector, and a waveguide which comprises a corelayer, a first cladding layer, and at least one adapter site for themovable light coupler formed in at least the first cladding layer. Insome embodiments, the detection system comprises a light source.

In some embodiments, the movable light coupler is able to localize anobject to the at least one adapter site formed in at least the firstcladding layer of the waveguide. In some embodiments, the adapter sitefor the movable light coupler is a nanowell. In some embodiments, themovable light coupler is a nano-scale particle. In some embodiments, themovable light coupler is a nano-scale sphere.

Furthermore, there is provided a method of detecting a single-moleculeobject, comprising the steps of a) introducing an incident light from alight source into a waveguide, thereby forming an excitation light inthe waveguide, b) localizing a single-molecule object on a movable lightcoupler, c) localizing the movable light coupler of (b) at an adaptersite for a movable light coupler formed in at least a first claddinglayer of the waveguide, and d) exciting, by the excitation light, asingle-molecule object localized on the movable light coupler, causingthe single-molecule object to emit a light to be detected by a lightdetector.

There is provided a method of detecting a single-molecule objectcomprising the steps of a) providing a detection apparatus comprising(i) a movable light coupler, (ii) a waveguide comprising a core layerand a first cladding layer, wherein at least one adapter site for themovable light coupler is formed in at least the first cladding layer,and (iii) a light detector; b) providing at least one binding moietycapable of binding a single-molecule object; c) localizing the at leastone binding moiety individually on the surface of the movable lightcoupler; d) providing a single-molecule object sample to one bindingmoiety localized on the movable coupler; e) localizing at the adaptersite the movable light coupler on which the at least one binding moietyand single-molecule object are localized; f) introducing an incidentlight from a light source into the waveguide, thereby forming anexcitation light in the waveguide; and g) exciting, by the excitationlight, a single-molecule object bound to the at least one binding moietylocalized on the movable light coupler, causing the single-moleculeobject to emit a light to be detected by a light detector.

There is provided a method of sequencing a nucleic acid, comprising thesteps of a) providing a detection apparatus comprising (i) a movablelight coupler, (ii) a waveguide comprising a core layer and a firstcladding layer, wherein at least one adapter site for the movable lightcoupler is formed in at least the first cladding layer, and (iii) alight detector; b) providing at least one nucleic acid molecule; c)localizing the at least one nucleic acid molecule individually on themovable light coupler; d) localizing at the adapter site the movablelight coupler on which at least one nucleic acid is localized; e)performing single molecule sequencing-by-synthesis of the at least onenucleic acid molecule, wherein the single molecule nucleic acidsequencing-by-synthesis produces an emitted light correlated to theidentity of at least one base in the nucleic acid; f) detecting theemitted light with the detector, resulting in an output signal; and g)processing the output signal to determine an identity of at least onebase comprised by the nucleic acid.

Additional objects and advantages will be set forth in part in thedescription which follows, and in part will be obvious from thedescription, or may be learned by practice of the embodiments. Theobjects and advantages of the invention will be realized and attained bymeans of the elements and combinations particularly pointed out in theappended claims.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the embodiments, as claimed.

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments of theinvention and together with the description, serve to explain theprinciples thereto.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the U.S. Patent and TrademarkOffice upon request and payment of the necessary fee.

FIG. 1 is a schematic view of a detection system consistent with certainembodiments.

FIG. 2 shows two schematic views of detection systems according to someembodiments.

FIG. 3 is a schematic view showing different adapter site designsconsistent with certain embodiments.

FIG. 4 is a schematic view showing a detection system according tocertain embodiments.

FIG. 5 shows schematic illustrations of a movable light coupler andwaveguide adapter site with surface modifications according to someembodiments.

FIG. 6 shows a schematic illustration of a movable light coupler andwaveguide adapter site with surface modifications according to someembodiments.

FIG. 7 is a schematic view of an exemplary detection system with amovable light coupler oriented at an adapter site in a specificorientation with the aid of a magnetic field.

FIG. 8 depicts an exemplary method of producing a single-strandedcircular target nucleic acid.

FIG. 9 is a schematic illustration of an exemplary movable light couplerwith a nucleic acid-synthesizing reaction complex localized on itssurface.

FIG. 10 is a schematic illustration of an exemplary movable lightcoupler with a nucleic acid-synthesizing reaction complex localized onits surface.

FIG. 11 is a schematic illustration of an exemplary movable lightcoupler with a nucleic acid-synthesizing reaction complex localized onits surface.

FIG. 12 depicts an exemplary method of producing a double-strandedcircular target nucleic acid.

FIG. 13 provides schematic illustrations of a denatured, double-strandedcircular target nucleic acid localized on the surface of a movable lightcoupler.

FIG. 14 shows schematic illustrations of an exemplary detection systemconfiguration used for simulation of stationary electromagnetic fieldsproduced by an incident excitation light wave.

FIG. 15 shows a contour map of the calculated stationary TE-modeelectric field for a simulated detection system.

FIG. 16 shows a contour map of the calculated stationary TM-modeelectric field for a simulated detection system.

FIG. 17 shows a contour map of the calculated stationary magnetic fieldfor a simulated detection system.

FIGS. 18 A, B, and C show contour maps of stationary electromagneticfields produced by an incident excitation light wave in detection systemconfigurations in which the nanowell does not extend into the corelayer, extends partially into the core layer, and extends fully throughthe core layer, respectively.

FIG. 19 shows schematic illustrations of an exemplary detection systemconfiguration used for simulation of stationary electromagnetic fieldsproduced by an incident excitation light wave.

FIG. 20 shows contour maps of the calculated stationary electric fieldfor a simulated detection system.

FIG. 21 shows contour maps of the calculated stationary electric fieldfor a simulated detection system.

FIG. 22 shows contour maps of the calculated stationary electric fieldfor a simulated detection system.

DETAILED DESCRIPTION OF THE EMBODIMENTS

Embodiments include a detection system and method of using the detectionsystem for detecting an object, such as a single-molecule object. Thedetection system is capable of detecting weak light emitted from theobject.

To achieve single-molecule detection, an optical system must be able toselectively excite the molecule of interest in a complicatedenvironment, and able to avoid the interference from the backgroundnoise and detect the weak light emitted from that single molecule. Toachieve single-molecule detection, and in one embodiment, a system mayneed to possess at least the following two criteria: 1) it has both aconfined excitation space and a confined observation space, and 2) theconfined excitation space and confined observation space should fully orpartially overlap, and the overlapping region should be small enough toensure that the light emitted from the target single molecule is higherthan the background to provide a detectable signal-to-noise ratio (SNR).For example, the volume of the overlapping region often must be on theorder of or smaller than a femtoliter. More particularly, the volume ofthe overlapping region often must be in the attoliter to zeptoliterrange. Moreover, it may also be important to prevent the excitationlight from reaching the detector.

Embodiments overcome the difficulties of loading a single-moleculesample to a detection system by use of a movable light coupler to carrya single-molecule sample to an adapter site for the movable lightcoupler formed in a waveguide. A confined space suitable forsingle-molecule detection may be formed after the movable light couplerdocks at the adapter site. The design of the movable light coupler andadapter site may prevent a second coupler from docking to the sameadapter site. In one embodiment, the single molecule sample, e.g., anenzyme, can be loaded to the coupler before the coupler is introduced tothe waveguide, and in one embodiment, all or a sample of the loadedcouplers can be pre-screened to ensure that each coupler carries one andonly one sample molecule. Because the sample molecules may remainassociated with the light couplers, the device may be reused by removingand discarding the couplers after detection. Because the sample moleculeis carried by the coupler, it is unnecessary to modify the surface ofthe waveguide in order to directly link the sample molecule to thesurface, thereby simplifying device manufacturing.

There is provided a system for detecting an object, such as asingle-molecule object, wherein the detection system comprises a movablelight coupler, a light detector, and a waveguide which comprises a corelayer, a first cladding layer, and at least one adapter site for themovable light coupler formed in at least the first cladding layer. Insome embodiments, the detection system comprises a light source.

In some embodiments, the movable light coupler is able to localize anobject to the at least one adapter site formed in at least the firstcladding layer of the waveguide, thereby localizing the object to bedetected inside the space in which the confined excitation space andconfined observable space overlap, i.e., a confined space suitable forsingle-molecule detection which is formed by docking of a movable lightcoupler to an adapter site. In some embodiments, the adapter site forthe movable light coupler is a nanowell. In some embodiments, themovable light coupler is a nano-scale particle. In some embodiments, themovable light coupler is a nano-scale sphere.

As used herein, the terms “confined excitation space,” “excitationspace,” and “excitation zone” all represent a space in which afluorophore or other light-emitting object will be excited and emitlight when entering.

As used herein, the terms “observable space” and “confined observablespace” represent a space in which light emitted by a fluorophore orother light-emitting object located within that space can be detected bythe detector.

As used herein, “confined space suitable for single-molecule detection”is used to signify a space in which excitation space and observablespace overlap. When a single-molecule light emitting object is localizedwithin the overlapping space, the object can be detected by thedetector.

As used herein, “movable light coupler” refers to a movable object thatcan alter a behavior of excitation light, including, for example, theshape of the light's intensity field distribution, the light's directionof travel, and the light's wavelength.

“Adapter site,” as used herein, refers to a space which is able toaccommodate a movable light coupler.

The term “docking,” as used in reference to a movable light coupler andan adapter site, refers to a movable light coupler fitting into anadapter site, thereby facilitating the formation of a confined spacesuitable for single-molecule detection.

In some embodiments, the movable light coupler is opaque to theexcitation light, whereby the confined space suitable forsingle-molecule detection is formed by the movable light couplerblocking the excitation light from the waveguide from spreading to thebulk space. In some embodiments, the movable light coupler has a surfacewhich is able to reflect excitation light, whereby the confined spacesuitable for single-molecule detection is formed in the region in whichthe movable light coupler reflects excitation light back toward thewaveguide.

In some embodiments, the movable light coupler is transparent orpartially transparent to excitation light, and placement of the movablelight coupler at the adapter site formed in at least the first claddinglayer of the waveguide allows an excitation zone to form around thesurface of the movable light coupler from a light wave propagating alongthe core layer of the waveguide and coupling to the movable lightcoupler, wherein a confined space suitable for single-molecule detectionis formed in the space between the movable light coupler and the adaptersite. In some embodiments, the refraction index of the movable lightcoupler is selected to enhance the level of light coupling. In someembodiments, the movable light coupler is transparent or partiallytransparent to excitation light, and the placement of the movable lightcoupler at the adapter site formed in at least the first cladding layerof the waveguide allows an excitation zone to form around the surface ofthe movable light coupler from a light wave propagating along the corelayer of the waveguide and coupling to the movable light coupler,thereby creating a confined space suitable for single-molecule detectionaround the surface of movable light coupler.

In some embodiments, the movable light coupler is able to absorb a firstexcitation light from the waveguide and then emit a second excitationlight.

There is provided a method of detecting a single-molecule object,comprising the steps of a) introducing an incident light from a lightsource into a waveguide, thereby forming an excitation light in thewaveguide, b) localizing a single-molecule object on the surface of amovable light coupler, c) localizing the movable light coupler of (b) atan adapter site for a movable light coupler formed in at least a firstcladding layer of the waveguide, and d) exciting, by the excitationlight, a single-molecule object localized on the movable light coupler,causing the single-molecule object to emit a light to be detected by alight detector. In some embodiments, localization of the movable lightcoupler at an adapter site for a movable light coupler formed in atleast a first cladding layer of the waveguide forms a confined spacesuitable for single-molecule detection.

In some embodiments, methods of detecting a single-molecule objectcomprise localizing a movable light coupler at an adapter site in aspecific orientation. In some embodiments, the methods compriselocalizing a movable light coupler at an adapter site in a specificorientation by a magnetic field. In further embodiments, the lightcoupler is localized at an adapter site in a specific orientation byapplication of an electric potential across the adapter site. In someembodiments, the light coupler is localized at an adapter site in aspecific orientation by introduction of one or more surfacemodifications at a light coupler adapter site which attract and/or repelsurfaces of a light coupler.

There is provided a method of detecting a single-molecule objectcomprising the steps of a) providing a detection apparatus comprising(i) a movable light coupler, (ii) a waveguide comprising a core layerand a first cladding layer, wherein at least one adapter site for themovable light coupler is formed in at least the first cladding layer,and (iii) a light detector; b) providing at least one binding moietycapable of binding a single-molecule object; c) localizing the at leastone binding moiety individually on the surface of the movable lightcoupler; d) providing a single-molecule object sample to one bindingmoiety localized on the movable coupler; e) localizing at the adaptersite the movable light coupler on which the at least one binding moietyand single-molecule object are localized; f) introducing an incidentlight from a light source into the waveguide, thereby forming anexcitation light in the waveguide; and g) exciting, by the excitationlight, a single-molecule object bound to the at least one binding moietylocalized on the movable light coupler, causing the single-moleculeobject to emit a light to be detected by a light detector. In someembodiments, localization at an adapter site of a movable light coupleron which the at least one binding moiety and single-molecule object arelocalized creates a confined space suitable for single-moleculedetection, wherein the single-molecule object to be detected islocalized within the confined space.

There is provided a method of sequencing a nucleic acid, comprising thesteps of a) providing a detection apparatus comprising (i) a movablelight coupler, (ii) a waveguide comprising a core layer and a firstcladding layer, wherein at least one adapter site for the movable lightcoupler is formed in at least the first cladding layer, and (iii) alight detector; b) providing at least one nucleic acid molecule; c)localizing the at least one nucleic acid molecule individually on themovable light coupler; d) localizing at the adapter site the movablelight coupler on which at least one nucleic acid is localized; e)performing single molecule sequencing-by-synthesis of the at least onenucleic acid molecule, wherein the single molecule nucleic acidsequencing-by-synthesis produces an emitted light correlated to theidentity of at least one base in the nucleic acid; f) detecting theemitted light with the detector, resulting in an output signal; and g)processing the output signal to determine an identity of at least onebase comprised by the nucleic acid.

A detection system may be used as part of a system for or in methods andprocesses of biomolecule detection, including nucleic acid hybridizationor sequencing for, e.g., whole-genome sequencing, transcriptionalprofiling, comparative transcriptional profiling, or geneidentification. Biomolecule detection can also include detection and/ormeasurement of binding interactions, e.g., protein/protein,antibody/antigen, receptor/ligand, and nucleic acid/protein. Theseapplications are useful for analytical or diagnostic processes andmethods

Hereinafter, embodiments will be described in detail with reference todrawings. Wherever possible, the same reference numbers will be usedthroughout the drawings to refer to the same or like parts.

1. Detection System

A detection system described herein can detect an object, such as asingle-molecule object. The object may be a source of luminescence, suchas a fluorescent dye molecule, a phosphorescent dye molecule, a quantumdot, or a light-emitting nanoparticle. The object may also be alight-scattering particle. In addition, the object may be a targetmolecule without light-emitting capability, but may be attached to alabeling object which is capable of emitting light (e.g., a fluorescentdye molecule, a phosphorescent dye molecule, or a quantum dot). Acertain labeling object may be capable of being attached to a specifictarget molecule. Thus, the target molecule may be identified via thelabeling object. More than one labeling object may be attached to onetarget molecule. The object may be a target molecule that does not havelight-emitting capability and is attached to multiple labeling objectswhich are capable of emitting light in a sequential order. (e.g., FRET,wherein light of a first wavelength is emitted from at least a firstexcited fluorescent molecule and is at least partially absorbed by asecond fluorescent molecule, which in turns emits a second light, i.e.,emitted light of a second wavelength).

1.1 Overview of the detection system

The detection system may comprise a movable light coupler, a detector,and a waveguide, wherein the waveguide comprises an adapter site for themovable light coupler.

The detection system may further comprise at least one light source,which can emit a light, which may then be at least partially coupledinto the waveguide as an excitation light to excite the object. Thelight source may be, for example, laser such as He—Ne laser and laserdiode (LD), light emitting diode (LED), organic light emitting diode(OLED), quantum dot light emitting diode (QLED), fiber light, or arcdischarge fluorescent lamp. The detection system may comprise a lightsource coupler. The light source coupler may couple at least part of thelight emitted from the at least one light source into the waveguide. Thelight source coupler may be, e.g., a prism coupler, a grating coupler, aside-injection coupler, a vertical-injection coupler, or aco-directional coupler.

The waveguide may be a channel waveguide or a planar waveguide. Thewaveguide may comprise a core layer and at least one cladding layer. Forexample, if the waveguide is a channel waveguide, it may comprise a corelayer and a cladding layer surrounding the core layer. As anotherexample, if the waveguide is a planar waveguide, it may comprise a corelayer and one cladding layer arranged on the core layer or two claddinglayers sandwiching the core layer. The core layer may have a higherrefractive index than the at least one cladding layer. The excitationlight may propagate in the core layer of the waveguide. Exemplarywaveguides and specific features thereof suitable for use in thedetection system are described in U.S. patent application Ser. No.12/720,352, filed Mar. 9, 2010; U.S. patent application Ser. No.12/801,503, filed Jun. 11, 2010; and U.S. patent application Ser. No.12/805,411, filed Jul. 29, 2010, each of which is incorporated herein byreference in its entirety.

The detection system may comprise a waveguide comprising at least oneadapter site for a movable light coupler. The adapter site may be formedin at least the at least one cladding layer of the waveguide. Theadapter site may be a nanowell comprising an upper opening and a bottomsurface, wherein the upper opening may be larger than the bottomsurface. The nanowell may extend through partial thickness of the atleast one cladding layer, full thickness of the at least one claddinglayer, full thickness of the at least one cladding layer and partialthickness of the core layer, or the full thickness of the at least onecladding layer and full thickness of the core layer. The lower boundaryof the effective excitation zone may be the bottom of the nanowell. Theupper boundary of the effective excitation zone may be defined by thedistance to which the excitation light can reach in the nanowell adaptersite in the direction perpendicular to the longitudinal direction of thecore layer (hereinafter, vertical direction).

Embodiments of the detection system encompass a movable light couplerwhich is able to localize a single-molecule object to the at least oneadapter site of the waveguide. The movable light coupler may be anano-scale particle. The movable light coupler may be a nano-scalesphere or a nonspheroidal nano-scale particle. When a movable lightcoupler docks at an adapter site in the waveguide, a confined excitationspace suitable for single-molecule detection (an effective excitationspace) may then form, and the object to be detected may be localizedwithin the confined space. When a movable light coupler docks at anadapter site, it may prevent a second movable light coupler from dockingat the same adapter site.

The movable light coupler may comprise at least one property by whichthe light coupler may be attracted to the adapter site, including, forexample, a surface property or a magnetic property to facilitatedocking. In some embodiments, the light coupler comprises at least oneproperty by which the light coupler may be localized at the at least oneadapter site in a specific orientation. Suitable properties by which thelight coupler may be localized at the at least one adapter site in aspecific orientation may include asymmetric surface properties. In someembodiments, the light coupler can localize a single-molecule object ina confined space near the surface of the core layer of the waveguidewithin the adapter site, wherein an object is localized in an effectiveexcitation zone formed within the adapter site from a light fieldinduced by a light wave propagating along the core layer of thewaveguide.

The core layer of the waveguide may have a higher refractive index thanthe at least first cladding layer of the waveguide. In some embodiments,the movable light coupler is made from a material having a refractiveindex substantially similar to the refractive index of a surroundingsolution or of the material of the at least first cladding layer of thewaveguide. In further embodiments, the movable light coupler is madefrom a material having a refractive index that is greater than therefractive index of the at least first cladding layer of the waveguide.In some embodiments, the movable light coupler is made from a materialhaving a refractive index that is substantially similar or equivalent tothat of the core layer of the waveguide. In some embodiments, the lightcoupler is able to couple an evanescent light field induced by a lightwave propagating along the core layer, whereby an effective excitationzone forms around the surface of the light coupler.

In some embodiments, the movable light coupler is opaque and can confineexcitation light at its surface, whereby the confined space suitable forsingle-molecule detection is formed by the movable light couplerblocking the excitation light from the waveguide from spreading to thebulk space. In some embodiments, the movable light coupler is reflectiveto light. In some embodiments, the movable light coupler is reflectiveto excitation light. In some embodiments, the movable light coupler isable to absorb excitation light emitted by the waveguide and then itselfemit a light which is able to excite molecules to be detected.

The waveguide component of the detection system may comprise a pluralityof adapter sites. Therefore, the system may also be used to monitor alarge number of objects.

The detection system may comprise a light detector detecting lightemitted from the object. The light detector may comprise an opticalsensor, which is capable of at least partially absorbing light incidentthereon and generating output signals in response to the light. Theoptical sensor may be, e.g., a p-n photodiode, a p-i-n photodiode, amulti-junction photodiode, an avalanche photodiode (APD), aphototransistor, a quantum-well infrared photodetector (QWIP), aphotoconductive type optical sensor, a photovoltaic type optical sensor,a thin-film on ASIC (TFA), a metal-semiconductor-metal (MSM)photodetector, a charge coupled device (CCD), a CMOS sensor, or acombination thereof.

In some embodiments, the light detector comprises a control circuit forcontrolling the operation of the light detector. The control circuit maycomprise a circuit of signal amplifier, ND convertor, integrator,comparator, logic circuit, readout circuit, memory, microprocessor,clock, and/or address.

The light detector may be arranged at a place that the light emittedfrom the object can reach. For example, the light detector may bearranged at the opposite side of the core layer with respect to theadapter site. That is, if the adapter site is arranged on one side ofthe core layer in the vertical direction, the light detector may then bearranged on the other side of the core layer in the vertical direction.The detection system may further comprise at least one filter betweenthe core layer and the detector.

A schematic view of an exemplary detection system is illustrated inFIG. 1. The detection system may comprise a movable light coupler 100and an integrated component comprising a planar waveguide 110, adetector 102, and an adapter site 104 for a movable light coupler,whereby the adapter site is accessible to a movable light coupler 100and a surrounding sample solution 120. The waveguide 110 may comprise acore layer 112, an upper cladding layer 114, and a lower cladding layer116. The planar waveguide 110 may be formed on a substrate (not shown).The light detector 102 may be formed on or in the substrate. A lightsource 130 may emit a light 135, which may be at least partially coupledinto the planar waveguide 110 by a light source coupler 140. Lightcoupled into the planar waveguide 110 may propagate along the core layerof the planar waveguide 110 and serve as the excitation light 145.

A schematic view of an exemplary detection system is illustrated in eachpanel of FIG. 2. In some embodiments, the movable light coupler 100 ismade of a material having a refractive index that is closer to therefractive index of a surrounding sample solution 120 or of the at leastfirst cladding layer 114 of the waveguide than to the refractive indexof the material of the core layer 112. In such embodiments, a light wavepropagating along the core layer of the waveguide from a light source(not shown) may induce an evanescent light field near the surface of thecore layer within the adapter site, thereby forming an effectiveexcitation zone 150 in the confined space at the bottom of the adaptersite (left panel). In further embodiments, the movable light coupler ismade from a material having a refractive index that is greater than therefractive index of the at least first cladding layer of the waveguideand/or that is substantially similar or equivalent to the refractiveindex of the core layer of the waveguide. In such embodiments, the lightcoupler may couple an evanescent light field induced near the surface ofthe core layer in the adapter site by a light wave propagating along thecore layer of the waveguide from a light source (not shown), therebyforming an effective excitation zone 160 in the confined space betweenthe movable light coupler and the core layer of the waveguide and aroundthe surface of the light coupler (right panel).

1.2 Components of Detection System

1.2.1 Waveguide

As shown in FIG. 1, in some embodiments, the planar waveguide 110 maycomprise a core layer 112, an upper cladding layer 114, and a lowercladding layer 116. The core layer 112 may comprise a material having arefractive index of n₂, such as silicon-titanium oxide(Si_(x)Ti_(1-x)O₂, where 0<x<1), titanium oxide, tantalum oxide, niobiumoxide, hafnium oxide, aluminum oxide, zirconium oxide, silicon nitride,aluminum nitride, titanium nitride, polycarbonate (PC), PMMA, or Su8.The upper and lower cladding layers 114 and 116 may comprise materialshaving a refractive index of n₃ and n₄, respectively. The materials forthe upper and lower cladding layers 114 and 116 may be the same or maybe different. Suitable material for the upper cladding layer 114 or thelower cladding layer 116 may comprise, for example, silicon oxide,magnesium fluoride, calcium fluoride, aluminum oxide, Su8, PMMA, orpolycarbonate. The refractive index n₂ of the core layer 112 may behigher than the refractive indices n₃ and n₄ of the upper and lowercladding layers 114 and 116.

For single-molecule detection, one may need to prevent the excitationlight from reaching the detector. In a planar waveguide, the surface ofthe core layer may not be as smooth as would be desired. The roughsurface of the core layer may scatter part of the excitation light. Ithas been estimated that, for a core layer having a surface roughness ofabout 0.3 nm, about 0.01% excitation light may be scattered and producethe noise. In order to reduce the noise coming from surface scatteringof excitation light propagating within the core, an excitation lightfilter may be added between the waveguide and detector to reduce theamount of scattered excitation light reaching the detector. In someembodiments, the filter is a multilayer interference filter. In someembodiments, the filter is a layer made of material that can absorbexcitation light.

In some embodiments, protection layer(s) may be included in thedetection system to absorb scattered excitation light and/or to blockthe ambient light from outside the detection system, so as to increasethe signal-to-noise (S/N) ratio, as described in U.S. application Ser.No. 12/801,503, filed Jun. 11, 2010, and in U.S. patent application Ser.No. 12/805,411, filed Jul. 29, 2010. A protection layer may be formedover an upper cladding layer, and/or a lower protection layer may beformed under a lower cladding layer. In some embodiments, a protectionlayer is made of an opaque material, such as metal or alloy. In someembodiments, a pinhole may be formed in a lower protection layer at aposition below the adapter site. Light emitted from an object in theeffective excitation zone in the adapter site may pass through thepinhole and be detected by a light detector below the lower protectivelayer.

1.2.2 Adapter Site

As exemplified if FIG. 1 and FIG. 2, at least one movable light coupleradapter site 104 may be formed in at least the upper cladding layer 114of the waveguide. The adapter site may be a nanowell. The upper openingof the nanowell may be larger than the bottom of the nanowell. The shapeof the nanowell is not limited. For example, the horizontal crosssection of the nanowell may have a circular shape, an oval shape, arectangular shape, a square shape, or a diamond shape. The size of thebottom of the nanowell adapter site is also not limited. For example,the size of the bottom of the nanowell may be smaller than about thewavelength of the excitation light. In some embodiments, the size of thebottom of the nanowell may be smaller than about one-half, aboutone-quarter, or about one-eighth of the wavelength of the excitationlight. As used herein, “size” may refer to diameter, length of the longaxis, or length of the long side if the horizontal cross section of thenanowell has a circular shape, an oval shape, or a rectangular shape. Ifthe horizontal cross section of the nanowell has a square or a diamondshape, “size” may refer to the length of the side. In one embodiment,the length (namely the diameter, length of the long axis, or length ofthe long side) of the upper opening of the nanowell may be about 1 toabout 10 μm and the diameter of the bottom of the nanowell may be about10 to about 500 nm, the angle of the sidewall of the nanowell relativeto the direction perpendicular to the bottom of the nanowell may be lessthan about 60 degrees. Such a configuration may ensure that only onesingle movable light coupler can enter a region near the bottom of thenanowell.

Part of the excitation light may enter the adapter site 104 and may,together with the spatial confinement of the adapter site 104, form aneffective excitation zone 150 in at least a portion of the adapter site,as exemplified in FIG. 1 and FIG. 2. It is to be understood thatreference number 150 in FIG. 1 indicates an approximate upper boundaryof the effective excitation zone. When an object enters the effectiveexcitation zone 150, it may be excited by the excitation light and emita light to be detected by the light detector 102. Outside the effectiveexcitation zone 150, an object may not be excited by the excitationlight, or its emitted light cannot reach the light detector. It is to beunderstood that, the dashed line in FIG. 1 does not limit the shape ofthe upper boundary of the effective excitation zone. For example, theupper boundary of an effective excitation zone may be in a curved shape.

Depending on different conditions, such as the position of the nanowelland/or the depth of the nanowell extending in the waveguide, a differenteffective excitation zone may be formed. In addition, theelectromagnetic field in the effective excitation zone may be, forexample, an evanescent field, a mixture of evanescent and travellingfields, or a travelling field, as described in more detail below.

FIG. 3 schematically shows, as examples, embodiments with differentnanowell adapter site designs. In some embodiments, a nanowell adaptersite may extend through partial thickness of the upper cladding layer(panel A). In some embodiments, a nanowell adapter site may extendthrough full thickness of the upper cladding layer (panel B). Fornanowells as shown in panels A or B, when the excitation lightpropagates in the core layer, although there may not be a travellinglight field component in the nanowell, part of the light travelling inthe core layer may penetrate slightly into the nanowell. The lightpenetrating into the nanowell may decay exponentially in the verticaldirection, forming an evanescent field. This evanescent field, togetherwith the spatial confinement of the nanowell, may form an effectiveexcitation zone in at least a portion of the nanowell near the corelayer.

In some embodiments, a nanowell may extend through the full thickness ofthe upper cladding layer and partial thickness of the core layer (FIG.3; panel C). In such an embodiment, a travelling field component mayappear in the nanowell, and together with an evanescent field, form aneffective excitation zone in the nanowell.

In some embodiments, a nanowell may extend through full thickness of theupper cladding layer and full thickness of the core layer (FIG. 3, panelD). In such an embodiment, most of the electromagnetic field forming anexcitation zone in the nanowell may be a travelling field.

For a planar waveguide comprising a nanowell as depicted in FIG. 3,panel B, because the bottom end of the nanowell is located on the uppersurface of the core layer, the volume of the effective excitation zonemay be equal to the effective region of the evanescent field, and may becalculated approximately using the following equation:V=π×(D/2)² ×hwhere D is the diameter of the bottom of the nanowell and h is thepenetration depth of the evanescent field in the nanowell. For example,if D and h are 100 nm and 100 nm, respectively, the calculated volume ofthe effective excitation zone is approximately 1×10⁻¹⁸ liter (1attoliter).

In some embodiments, a plurality of adapter sites may be formed in thewaveguide. In some embodiments, for each of the plurality of adaptersites, a light detector may be formed to detect the light emitted froman object in the effective excitation zone of the adapter site. In someembodiments, one light detector may be used to detect the light emittedfrom objects in the effective excitation zones of a plurality of adaptersites.

1.2.3 Movable Light Coupler

Embodiments encompass a movable light coupler that may be capable oflocalizing a single-molecule object at an adapter site formed in atleast a first cladding layer of a waveguide. The movable light couplermay localize on its surface at least one binding moiety capable ofbinding a single-molecule object to be detected. A binding moiety may bea single molecule or molecular complex (e.g., a receptor, an antibody,an enzyme, or a multimeric complex such as a reaction complex comprisingan enzyme) which is capable of binding the object. A single-moleculeobject to be detected may bind to the binding moiety localized on thesurface of a movable light coupler which is positioned at an adaptersite, thereby localizing the object, via the binding moiety and lightcoupler, in a confined space for effective signal excitation andobservation. The movable light coupler may have only one binding moietylocalized on its surface, such that if binding of the single-moleculeobject to the surface-localized binding moiety is detected, the numberof objects detected at any given moment may be no greater than thenumber of objects that can simultaneously bind to the binding moiety.Thus, where a binding moiety binds only one object at a time, thedetection system can detect a single object binding to the bindingmoiety localized on the surface of the movable light coupler.

An object that is “localized” on the surface of a movable light coupler,as used herein, includes an object that is nonspecifically adsorbed onthe surface of a movable light coupler and an object that is tethered tothe surface of a movable light coupler via one or more covalent linkagesor via noncovalent interactions.

In some embodiments, the movable light coupler is a nano-scale particle.In some embodiments, the light coupler is a nano-scale sphere. Thenano-scale sphere may have a diameter of from about 40 nm to 1000 nm orfrom about 1/10 to twice the wavelength of the excitation light. Thesize of the nano-scale sphere may be decided in accordance with the sizeof the light detector. For example, the size of the nano-scale spheremay be chosen such that a single light detector is only capable ofdetecting the light emanating from only one sphere. In some embodiments,the size of the nano-scale sphere and the shape of the adapter site arechosen such that the nanosphere may be positioned at the adapter site ata distance of between about 10 nm and 200 nm from the bottom surface ofthe adapter site. In further embodiments, the light coupler is anonspheroidal nano-scale particle. In some embodiments, the nano-scaleparticle is a bar-like particle. The “length” of a movable light couplerparticle refers to the distance from one end of the light coupler to theopposite end at the widest point of the light coupler. For example, thelength of a spherical light coupler corresponds to its diameter, and thelength of a bar-like particle is the distance between the far ends ofthe bar.

The movable light coupler may be a homogenous solid, a colloidal orporous solid, or a solid composed of a material with a polymer backbone.In some embodiments, the multifunctional movable light coupler comprisesone or more metal materials, including, for example, gold (Au), silver(Ag), cupper (Cu), platinum (Pt), nickel (Ni), chromium (Cr), or a metalalloy. In some embodiments, the light coupler comprises one or moreoxide materials, including, for example TiO₂, Ta₂O₅, Nb₂O₅, SiO₂, HfO₂,Al₂O₃, ZrO₂, ZnO, V₂O₅, CeO₂, CdO, Fe₂O₃, Fe₃O₄, Cu₂O, CuO, In₂O₃,La₂O₃, MoO₃, or WO₃. In further embodiments, the light coupler comprisesone or more sulfide materials, including, for example, CdS, ZnS, PbS,Au₂S, or Ag₂S. In some embodiments, the light coupler comprises one ormore selenide materials, including, for example, CdSe, ZnSe, or PbSe. Insome embodiments, the light coupler comprises one or more nitridematerials, including, for example, Si₃N₄, TiN, BN, and GaN. In furtherembodiments, the light coupler comprises one or more polymer materials,including, for example, polystyrene, a polyethyleneimine, apolyphosphazene, polylactide, polylactide-co-glycolide,polycaprolactone, a polyanhydride, polymaleic acid and its derivatives,polyalkylcyanoacrylate, polyanhydride oxybutyrate, polycarbonate,polyorthoester, polyethylene glycol, poly-L-lysine, polyglycolide,polymethylmethacrylate, polyvinylpyrrolidone, or copolymers thereof.

In some embodiments, the movable light coupler has a core-shellnanostructure. The core material may comprise one or more metalmaterials, including, for example, gold (Au), silver (Ag), cupper (Cu),platinum (Pt), nickel (Ni), chromium (Cr), or a metal alloy. In someembodiments, the core material comprises one or more oxide materials,including, for example TiO₂, Ta₂O₅, Nb₂O₅, SiO₂, HfO₂, Al₂O₃, ZrO₂, ZnO,V₂O₅, CeO₂, CdO, Fe₂O₃, Fe₃O₄, Cu₂O, CuO, In₂O₃, La₂O₃, MoO₃, or WO₃. Insome embodiments, the core material comprises one or more sulfidematerials, including, for example, CdS, ZnS, PbS, Au₂S, or Ag₂S. Infurther embodiments, the core material comprises one or more selenidematerials, including, for example, CdSe, ZnSe, or PbSe. In someembodiments, the core material comprises one or more nitride materials,including, for example, SiN or GaN. In further embodiments, the corematerial comprises one or more polymer materials, including, forexample, polystyrene, a polyethyleneimine, a polyphosphazene,polylactide, polylactide-co-glycolide, polycaprolactone, apolyanhydride, polymaleic acid and its derivatives,polyalkylcyanoacrylate, polyanhydride oxybutyrate, polycarbonate,polyorthoester, polyethylene glycol, poly-L-lysine, polyglycolide,polymethylmethacrylate, polyvinylpyrrolidone, or copolymers thereof.

The shell of a core-shell nanostructure light coupler may comprise oneor more metal materials, including, for example, gold (Au), silver (Ag),cupper (Cu), platinum (Pt), nickel (Ni), chromium (Cr), or a metalalloy. In some embodiments, the shell material comprises one or moreoxide materials, including, for example TiO₂, Ta₂O₅, Nb₂O₅, SiO₂, HfO₂,Al₂O₃, ZrO₂, ZnO, V₂O₅, CeO₂, CdO, Fe₂O₃, Fe₃O₄, Cu₂O, CuO, In₂O₃,La₂O₃, MoO₃, or WO₃. In some embodiments, the shell material comprisesone or more sulfide materials, including, for example, CdS, ZnS, PbS,Au₂S, or Ag₂S. In further embodiments, the shell material comprises oneor more selenide materials, including, for example, CdSe, ZnSe, or PbSe.In some embodiments, the shell material comprises one or more nitridematerials, including, for example, SiN or GaN. In further embodiments,the shell material comprises one or more polymer materials, including,for example, polystyrene, a polyethyleneimine, a polyphosphazene,polylactide, polylactide-co-glycolide, polycaprolactone, apolyanhydride, polymaleic acid and its derivatives,polyalkylcyanoacrylate, polyanhydride oxybutyrate, polycarbonate,polyorthoester, polyethylene glycol, poly-L-lysine, polyglycolide,polymethylmethacrylate, polyvinylpyrrolidone, or copolymers thereof.

In some embodiments, the movable light coupler is made from a materialhaving a refractive index that is closer to the refractive index of thematerial of the first cladding layer of the waveguide than to therefractive index of the material of the core layer of the waveguide. Insome embodiments, the movable light coupler is made from a materialhaving a refractive index that is closer to the refractive index of asurrounding sample solution than to the refractive index of the materialof the core layer of the waveguide. In some embodiments, the movablelight coupler is made from a material having a refractive index that isintermediate between the refractive index of the first cladding layer ofthe waveguide and the refractive index of the core layer of thewaveguide. In further embodiments, the light coupler is made from amaterial having a refractive index that is substantially similar to therefractive index of the core layer of the waveguide. In someembodiments, the light coupler is made from a material having arefractive index that is equivalent to the refractive index of the corelayer.

In some embodiments, the movable light coupler is composed of SiO₂,having a refractive index of 1.487. In some embodiments, the movablelight coupler is composed of polystyrene, having a refractive index of1.59. In further embodiments, the light coupler is composed of TiO₂,having a refractive index of 2.0. In some embodiments, the light coupleris composed of Fe₃O₄, having a refractive index of 2.4. In still furtherembodiments, the light coupler is composed of Ta₂O₅, having a refractiveindex of 2.26.

In some embodiments, the light coupler has a core-shell structure,wherein the shell material is gold (Au), having a refractive index of1.28. In some embodiments, the shell material is silver (Ag), having arefractive index of 0.135. In further embodiments, the shell material isplatinum (Pt), having a refractive index of 1.9. In some embodiments,the shell material is aluminum (Al), having a refractive index of 0.714.In still further embodiments, the shell material is cobalt (Co), havinga refractive index of 1.86. In some embodiments, the shell material isnickel (Ni), having a refractive index of 1.66.

In some embodiments, the movable light coupler has an appropriate sizeand a refractive index sufficiently similar to the refractive index ofthe material of the core layer of the waveguide such that the lightcoupler is able to couple light from a waveguide when placed at anadapter site in the waveguide. In such embodiments, an induced lightfield may form around the surface of the movable light coupler, therebyforming an effective excitation zone around the light coupler, wherein amolecule can be excited to emit fluorescent light within a certaindistance of the surface of the light coupler.

The intensity of the excitation light field induced around the surfaceof the movable light coupler may be controlled by tuning the opticalwaveguide's electric field in the surrounding environment, by selectingappropriate characteristics (e.g., material composition, shape, andsize) for the light coupler, and by configuring the shape of the adaptersite. In embodiments in which the movable light coupler is a sphere, theintensity of the excitation light field at the surface of the lightcoupler can be calculated with the following formula:

$\begin{matrix}{{P = {1 - \frac{( \frac{I_{\max}}{I_{i}} )}{1 + {( \frac{2{??}}{\pi} )^{2}{\sin^{2}( \frac{\theta}{2} )}}}}},} & ( {{equation}\mspace{14mu} 1} )\end{matrix}$where P is the optical power of the excitation light field on the spheresurface, ℑ (Finesse) is determined by the equation

${{??} = \frac{\pi\sqrt{r}}{( {1 - r} )}},$r is determined by the equationr=√{square root over ((1−κ)exp(−πRα _(ring)))}I_(max)/I_(i) is determined by the equation

${\frac{I_{\max}}{I_{i}} = \frac{\kappa\lbrack {1 - {\exp( {{- 2}\pi\; R\;\alpha_{ring}} )}} \rbrack}{\lbrack {1 - \sqrt{( {1 - \kappa} ){\exp( {{- \pi}\; R\;\alpha_{ring}} )}}} \rbrack^{2}}},$θ is determined by the equationθ=N_(ring)k₀2πRand where R is the radius of the curvature of the sphere, α_(ring) isthe sphere's mode power decay coefficient, N_(ring) is the sphere'sequilibrium refractive index, κ is the power coupling coefficient, andk₀=2π/λ₀ (where λ₀ is the free-space wavelength. In a resonancesituation, where the light energy will transfer completely into thespherical light coupler, N_(ring)k₀2πR=2mπ, where m is an integer,κ=1−exp(−2πR₁α_(ring)) (where R₁ is the outer bending radius), and P=1.The term “critical coupling” is used herein to describe this resonancesituation.

In some embodiments, an optical property of the light coupler changeswhen the light coupler is surrounded by certain molecules within aspecific range. In some embodiments, the optical property that changeswhen the light coupler is surrounded by certain molecules within aspecific range is refractive index, light-absorbing capability, thewavelength of light absorbed by the coupler, or the direction of lightpropagating through the light coupler.

In some embodiments, one or more regions of the surface of the movablelight coupler are modified. For example, the entire surface ofnano-scale sphere light coupler may be modified. Surface modification isdistinct from the shell material of a light coupler with a core-shellstructure, i.e., a core-shell light coupler comprising surfacemodification has modification of the outside surface of the shellmaterial. In a further example, the surface of one hemisphere of anano-scale sphere light coupler may be modified while the remaininghemisphere is unmodified. The surface of the light coupler may be coatedover its entire surface or at least a portion of its surface with one ormore heterogeneous materials by chemical modification techniques. Asurface modification may serve to localize the movable light coupler atan adapter site. Asymmetric surface modification, e.g., modification onone surface only, or different modification on opposite surfaces, mayserve to localize the movable light coupler at an adapter site in aspecific orientation. A surface modification may also serve to localizea single-molecule object at a particular region of the surface of thelight coupler, whereby such a region may be oriented to face the corelayer of the waveguide, thereby localizing the object and any reactioninvolving the object in a confined space between the movable lightcoupler and the surface of the adapter site near the core layer of thewaveguide. A schematic illustration of an exemplary detection systemcomprising a nano-scale sphere light coupler particle which is modifiedon one hemisphere with oligonucleotide primers is shown in FIG. 4. Thenano-scale sphere light coupler 100 is modified on one half of itssurface with oligonucleotide primers capable of hybridizing to sequencesembedded in a replicating DNA strand of a DNA synthesizing reactioncomplex 200. Positioning of the light coupler 100 at the adapter site104 with the oligonucleotide-modified surface of the light couplerfacing the core layer of the waveguide localizes the reaction complex200 in the confined space 170 in the bottom of the nanowell adapter site104.

In some embodiments, the modification of one or more regions of thesurface of the movable light coupler is chemical modification. In someembodiments, the chemical modification is covalent linkage of afunctional group to the surface of the light coupler. Acovalently-linked functional group may be a hydrophobic group or ahydrophilic group. Suitable hydrophobic groups include, for example,—C_(x)(H₂)_(x)CH₃, —C₆H₆, an epoxy group, —Si(C_(x)H_(x+1))₂ (derivedfrom a compound having the formula H₃—Si(C_(x)H_(x+1))₂, such asN-octylsilane), —O—Si(C_(x)H_(x+1))₂ (derived from a compound having theformula R₃—O—Si(C_(x)H_(x+1))₂, such as trimethoxy(octyl)silane), andthe like. In some embodiments, the light coupler is a homogenous solidparticle composed of a metal material or is a core-shell particlecomprising a metal shell material, and a hydrophobic group is covalentlylinked to the metal material via a sulfur, an amine, carboxyl, orphosphate linkage. In some embodiments, the light coupler is ahomogenous solid particle composed of a metal oxide or SiO₂ material oris a core-shell particle comprising a metal oxide or SiO₂ shellmaterial, and a hydrophobic group R is covalently linked as a —Si—Rgroup to the oxygen atoms of the metal oxide or SiO₂ material. In someembodiments, the covalently-linked functional group is a hydrophilicgroup, including, for example, —NH₂, —OH, —CO₂H, —OSO₃H. For example, insome embodiments, the light coupler is a homogenous solid particlecomposed of a metal oxide or SiO₂ material or is a core-shell particlecomprising a metal oxide or SiO₂ shell material, and an —OH group iscovalently linked to the metal oxide or SiO₂ material. Suitablehydrophilic groups further include charged groups, including, forexample, positively-charged groups such as —NH₃ ⁺, or negatively-chargedgroups such as —CO₂ ⁻ or —OSO₃ ⁻. In some embodiments, acovalently-linked functional group is a magnetic functional group.Suitable magnetic groups include, for example, —Fe₃O₄, —Fe₂O₃, —FePt,—FeNi, —FeCo, —Mg, —Co, —Ni, and the like. In some embodiments, acovalently-linked functional group is a fluorescent functional group.Suitable fluorescent groups include, for example, molecular dyes such as-FITC, —Rhodamine 6G (—Rh6G), -Cy3, and -Cy5, and the like, andnanoparticles/quantum dots, such as —CdSe, —ZnS, —PbS, —PbSe, and thelike. In some embodiments, a surface of the movable light coupler iscovalently modified with biotin, streptavidin, avidin, or the like.

In further embodiments, the chemical modification is a noncovalentmodification. The noncovalent modification may be a coating with apolymer material. In some embodiments, for example, the light coupler isa homogenous solid particle composed of a metal material or is acore-shell particle comprising a metal shell material, and a surface ofthe light coupler is coated with a hydrophilic polymer, such aspolyethylene glycol (PEG).

In some embodiments, only one region of the surface of the movable lightcoupler is modified, while the remainder of the surface of the lightcoupler is unmodified. In some embodiments, the modified region of thesurface of the movable light coupler is from about 10 to 90% of thesurface of the movable light coupler. “About 10 to 90% of the surface ofthe movable light coupler” as used to describe such embodiments is meantto signify that the modified region of the surface of the movable lightcoupler may be anywhere from slightly less than 10% to slightly morethan 90% of the surface of the light coupler. In further embodiments,the modified region of the surface of the light coupler is less than 10%of the surface of the light coupler. In yet further embodiments, themodified region of the surface of the light coupler is more than 90% ofthe surface of the light coupler.

In some embodiments, two regions of the surface of the movable lightcoupler are modified, as schematized in FIG. 5A, showing modifiedsurface 1 and modified surface 2. In some embodiments, the light couplercomprises two regions of surface modification with functional groups orcoatings having opposing properties. For example, one surface of thelight coupler may be modified to have a hydrophobic surface character,while the opposite surface may be modified to have a hydrophilic surfacecharacter. In further embodiments, one surface of the light coupler ismodified with a positively-charged group, while the opposite surface ismodified with a negatively-charged group. In some embodiments, onesurface of the light coupler is modified to attract and retain DNA,e.g., the surface is modified with a positively-charged functional groupor is modified with an oligonucleotide capable of hybridizing tosequences in a target DNA molecule, while the other surface of the lightcoupler does not attract DNA.

In further embodiments, the movable light coupler comprises two regionsof surface modification with functional groups or coatings havedifferent types of properties. For example, in some embodiments, oneregion of the surface of a movable light coupler is modified with amagnetic functional group, while the opposite surface of the movablelight coupler is modified with a fluorescent functional group.

In some embodiments, the surface of an adapter site formed in at leastthe first cladding layer of a waveguide comprises one or more surfacemodifications. The waveguide may comprise a first cladding layer and asecond cladding layer, as schematized in FIG. 5B, wherein the first(lower) cladding layer and a surface of the core layer (not shown) atthe bottom of the adapter site comprise a surface modification 3 thatattracts surface modification 1 on the movable light coupler 100 and/orthat repels surface modification 2 on the movable light coupler 100, andwherein the second (upper) cladding layer comprises a surfacemodification 4 that is compatible with surface modification 2 on themovable light coupler 100. The waveguide may comprise a first claddinglayer that comprises both surface modifications 3 (together with asurface of the core layer at the bottom of the adapter site) and 4, asschematized in FIG. 6, wherein surface modification 3 attracts surfacemodification 1 on the movable light coupler 100 and/or repels surfacemodification 2 on the movable light coupler 100, and wherein surfacemodification 4 is compatible with surface modification 2 on the movablelight coupler 100. For example, surface modifications 1 and 3schematized in FIG. 5 and FIG. 6 may be hydrophilic in nature, whilesurface modifications 2 and 4 are hydrophobic in nature. In someembodiments, surface 3 of the adapter site 104 is hydrophilic,comprising a member chosen from silicon, silica, metal, or metal oxide,and surface 4 is hydrophobic. However, if a surface of the adapter site104 is made of a material with hydrophilic property, it may be modifiedto be hydrophobic. For example, if a surface of the adapter site 104 ismade of silicate or metal with a hydrophilic nature, it may be modifiedto be hydrophobic using, for example, R1_(x)—Si(O—R2)_(4-x) (where R1 isa hydrophobic group, such as alkyl chain —(CH₂)_(n)—CH₃, and R2 isC_(n)H_(2n+1), and where x and n are integers and 1≦X≦3) or using, forexample, polymers with a functional group chosen from —COOH, —PO₃H₂,—SH, or —NH₂. As another example, if a surface of the adapter site 104is made of metal oxide with hydrophilic property, it may be modified tobe hydrophobic using, for example, R1_(x)—Si(O—R2)_(4-x) (where R1 is ahydrophobic group, such as alkyl chain —(CH₂)_(n)—CH₃, and R2 is—C_(n)H_(2n+1), and where x and n are integers and 1≦x≦3) or using, forexample, polymers with a functional group chosen from —COOH, —PO₃H₂,—SH, or —NH₂. By making an upper surface of the adapter site 104hydrophobic but keeping the bottom surface of the adapter site 104hydrophilic, a movable light coupler comprising one hydrophobic surfaceand one hydrophilic surface (see descriptions of light coupler surfacemodification below) may be positioned at the adapter site in a specificorientation with the hydrophilic surface being positioned in theeffective excitation zone near the bottom of the adapter site ratherthan facing upwards or toward a sidewall surface of the adapter site.Thus, a molecule localized on one region of the surface of the movablelight coupler (e.g., in this example, the hydrophilic surface), or amolecule from a sample solution 120 which interacts with the moleculelocalized on the surface of the light coupler, may be effectivelyexcited by the excitation light entering the effective excitation zonein the confined space near the bottom of the adapter site.

With further reference to embodiments schematized in FIG. 5 and FIG. 6,in some embodiments, surface modifications 1 and 3 are surfacemodifications with groups having opposite charges, i.e., surface 1 ispositively charged and surface 3 is negatively charged, or vice versa.

In some embodiments, at least a region of the surface of the movablelight coupler is modified with oligonucleotides. A schematic view of anexemplary detection system comprising a movable light coupler comprisinga surface modification with oligonucleotides is illustrated in FIG. 4.In some embodiments, the oligonucleotides are complementary to thesequence of a sequencing primer utilized in the nucleic acidsynthesizing reaction. In further embodiments, the oligonucleotides haverandom sequences. The oligonucleotides may be from 10 to 100 nucleotidesin length. For example, the oligonucleotides may be from 10 to 20, 20 to30, 30 to 40, 50 to 60, 60 to 80, or 80 to 100 nucleotides in length. Itis to be understood that these nucleotide length ranges are approximate,and that a specified range for nucleotide length includes a number ofnucleotides that is “about” in this range, e.g., oligonucleotides from10 to 100 nucleotides in length includes oligonucleotides from about 10to 100 nucleotides in length. The length of the oligonucleotides may beless than 10 nucleotides. The oligonucleotides may be, for example, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, or more than 30 nucleotides in length. In someembodiments, the length of the oligonucleotides corresponds to thelength of the sequencing primer. In some embodiments, theoligonucleotides are shorter in length than the sequencing primer. Theoligonucleotides may be linked directly to the movable light coupler, orthey may be linked to a moiety by which the oligonucleotides may becoupled to a movable light coupler, e.g., a biotin group, which may bindto a streptavidin or avidin linked to the surface of a movable lightcoupler.

A region of surface modification may be introduced on the movable lightcoupler using manufacturing processes known in the art. For example, aregion of surface modification may be introduced by temporarily maskingone portion of the light coupler while the remaining portion of thesurface of the light coupler is modified. For example, one hemisphere ofa nano-scale sphere light coupler may be masked while the otherhemisphere receives a surface modification. In some embodiments, thelight coupler is partially coated with a heterogenous material by aprocess of aligning one or more light couplers on a substrate (e.g., aglass or silicon substrate), depositing a heterogenous material on thesurface of the coupler aligned on a substrate, and then utilizing alift-off method to remove the modified light coupler from the substrate.Alignment of a light coupler on a substrate can be performed byspin-coating, dip-coating, embedding, nanoimprinting, nano ink-printing,use of nano-particle self assembly technology (e.g., self-assembly ofnanoparticles on a substrate pre-patterned by chemical lithography), orby similar methods. Deposition of a heterogeneous material on the lightcoupler may be performed by such methods as sputter deposition,magnetron sputter deposition, evaporation, atomic layer deposition,chemical vapor deposition, physical vapor deposition (PVD), electronbeam (e.g., e-gun) deposition, plasma deposition, laser flashevaporation (e.g., evaporated metal deposition), or the like. Thelift-off method may be ultrasonic agitation, chemical treatment (e.g.,treatment with acetone), magnetic lift-off, or physically peeling awaythe deposited layer with the aid of a razor blade. Exemplarymanufacturing processes suitable for the production of movable lightcoupler particles having asymmetric surface modification are describedin Park, H., et al., “Multifunctional nanoparticles for photothermallycontrolled drug delivery and magnetic resonance imaging enhancement,”SMALL 4(2):192-196 (2008); International Patent Publication Number WO2008/002101, entitled “Multi-functional nanoparticlespartially-deposited with gold film”; Anker, J. N., et al.,“Magnetically-Modulated Optical Nanoprobes (MagMOONs) and Systems,”JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 293:655-662 (2005); Perro,A., et al., “Design and synthesis of Janus micro- and nanoparticles,”JOURNAL OF MATERIALS CHEMISTRY 15: 3745-3760 (2005); McNaughton, B. H.,et al., “Fabrication of uniform half-shell magnetic nanoparticles andmicrospheres with applications as magnetically modulated opticalnanoprobes,” arXiv:cond-mat/0506418v1, Jun. 16, 2005, 1-6; and Wu, L.Y., et al., “Bioinspired nanocorals ” with decoupled cellular targetingand sensing functionality, SMALL 6(4):503-507 (2010), each of which isincorporated herein by reference in its entirety.

1.2.4 Directed Localization of the Movable Light Coupler at an AdapterSite

In some embodiments, a movable light coupler particle with asurface-localized binding moiety for a single-molecule object (i.e., amolecule or molecular complex capable of binding a single-moleculeobject) is localized at an adapter site formed in a waveguide using anelectric field, a magnetic field, or using hydrophilic surface characteror other chemical character according to the design of the lightcoupler.

A light coupler which comprises magnetic materials and/or is modifiedwith magnetic functional groups on its surface may be localized at anadapter site by application of a magnetic field to the adapter site, asschematized in FIG. 7. For example, micro-fabricated coils may be placedunder the adapter site. When an electric current is passed through themicro-fabricated coils, the coils may generate a magnetic field whichdirects a light coupler present in the sample solution into an adaptersite and traps the light coupler against the bottom of the adapter site.A suitable method for trapping magnetic nano-particles is described inRamadan, Q., et al., “Customized trapping of magnetic particles,”MICROFLUID NANOFLUID 6:53-62 (2009), which is incorporated herein byreference in its entirety.

A light coupler that is modified with charged functional groups may belocalized at an adapter site by application of an electric potentialacross the adapter site. For example, micro-fabricated electrodes may bepositioned at the bottom of an adapter site in the form of a glass slidecoated with a layer of conducting material to act as an electrode.Application of an electric current, e.g., direct current, to theelectrodes generates an electric field through the adapter site whichacts as an electrophoretic particle entrapment system that directs themodified light coupler into the adapter site. Suitable electrophoretictechniques for directing nano-particles to specific detection sites aredescribed in Han, J., et al., “High performance electrophoresis systemfor site-specific entrapment of nanoparticles in a nanoarray”, PROC.SPIE 7574:75740 L (2010) and in Velev, O. D., et al.,“Particle-localized AC and DC manipulation and electrokinetics”, ANNU.REP. PROG. CHEM., SECT. C, 105:213-246 (2009), each of which isincorporated herein by reference in its entirety.

1.2.5 Other Optional Components of the System

In some embodiments, as shown in FIG. 4, an optical filter 118 may bearranged between the core layer 112 and the detector 102. In someembodiments, the filter may be arranged between a lower cladding layer(not shown in FIG. 4) and the light detector 102. In some embodiments,the optical filter may be arranged between a lower protection layer (notshown) and the light detector 102. In some embodiments, a lowerprotection layer itself may serve as an optical filter. An opticalfilter may allow a light with a wavelength within a certain range topass through but at least partially block a light with a wavelengthoutside the certain range. Therefore, by properly choosing the opticalfilter 118, the light emitted from the object may be allowed to passthrough but the noise caused by the excitation light is reduced, so asto improve the S/N ratio.

The movable light coupler and object to be detected may be contained ina sample solution 120, which may fill the adapter site 104. In someembodiments, a microfluidic channel (not shown) may be used to conductthe sample solution into the adapter site. The microfluidic channel maybe designed in a way that the target objects pass through the adaptersite one at a time, so as to realize a flow-cytometry-like detection. Insome embodiments, a cover (not shown) may be formed over the detectionsystem to contain the sample solution and/or to block the ambient light.

In some of the above-described figures schematically showing thestructures of detection systems, for simplicity, some components are notshown. For example, each panel of FIG. 2 only shows the movable lightcoupler 100, the waveguide 110 and the adapter site 104 components ofthe detection system. Other components of the detection system are notshown. It is to be understood that the detection systems shown in thesefigures may also comprise other components as disclosed herein. Forexample, the detection system shown in each panel of FIG. 2 may alsocomprise a light detector, a cover, a protection layer(s), a lightsource, and/or an optical filter.

2. Methods of Detection and Applications

In another aspect, the disclosure relates to a method of detecting anobject, such as a single-molecule object, using the detection system asdisclosed herein. As used herein, the term “single-molecule object”includes an object composed of a single molecule and a single objectcomposed of multiple noncovalently linked molecules, such as a singlemultimeric polypeptide complex or a single segment of double-strandedDNA. A sample solution comprising the object may be filled in theadapter site formed in the waveguide of the detection system. Anincident light emitted by a light source may be at least partiallycoupled by a light coupler into the waveguide and propagate in the corelayer of the waveguide. The light coupled into the waveguide may serveas an excitation light, and may at least partially couple to a movablelight coupler localized at an adapter site formed in the waveguide. Theobject, when entering the effective excitation zone at the bottom of theadapter site and/or surrounding the surface of the light couplerlocalized at the adapter site, may be excited by the excitation lightand emit a light to be detected by a light detector.

Furthermore, there is provided a method of detecting a single-moleculeobject, comprising the steps of a) introducing an incident light from alight source into a waveguide, thereby forming an excitation light inthe waveguide, b) localizing a single-molecule object on a movable lightcoupler, c) localizing the movable light coupler of (b) at an adaptersite for a movable light coupler formed in at least a first claddinglayer of the waveguide, and d) exciting, by the excitation light, asingle-molecule object localized on the movable light coupler, causingthe single-molecule object to emit a light to be detected by a lightdetector. In some embodiments, localization of the movable light couplerat an adapter site for a movable light coupler formed in at least afirst cladding layer of the waveguide forms a confined space suitablefor single-molecule detection.

Furthermore, there is provided a method of detecting a single-moleculeobject comprising the steps of a) providing a detection apparatuscomprising (i) a movable light coupler, (ii) a waveguide comprising acore layer and a first cladding layer, wherein at least one adapter sitefor the movable light coupler is formed in at least the first claddinglayer, and (iii) a light detector; b) providing at least one bindingmoiety capable of binding a single-molecule object; c) localizing the atleast one binding moiety individually on the surface of the movablelight coupler; d) providing a single-molecule object sample to onebinding moiety localized on the movable coupler; e) localizing at theadapter site the movable light coupler on which the at least one bindingmoiety and single-molecule object are localized; f) introducing anincident light from a light source into the waveguide, thereby formingan excitation light in the waveguide; and g) exciting, by the excitationlight, a single-molecule object bound to the at least one binding moietylocalized on the movable light coupler, causing the single-moleculeobject to emit a light to be detected by a light detector. In someembodiments, localization at an adapter site of a movable light coupleron which the at least one binding moiety and single-molecule object arelocalized creates a confined space suitable for single-moleculedetection, wherein the single-molecule object to be detected islocalized within the confined space.

In some embodiments, methods of detecting a single-molecule objectrelate to methods of detecting the interaction of target moleculesand/or molecular complexes, e.g., receptor ligands and receptorcomplexes, antigens and antibodies, or free nucleotide triphosphates andnucleic acid-synthesizing reaction complexes. In some embodiments,methods include detection of a labeled molecule. In some embodiments,the label is a fluorescent label. In some embodiments, the label is afluorescent molecule. In further embodiments, the label is a fluorescentprotein. In certain embodiments, the label is a quantum dot. In someembodiments, the label is a member of a FRET donor/acceptor pair. Thedetection system, and method of using the same, may be applied to, e.g.,nucleic acid detection, DNA sequencing, biomarker identification, orflow cytometry. The detection systems can detect and process lowintensity light signal, which makes single-molecule detection possible.

Furthermore, there is provided a method of sequencing a nucleic acid,comprising the steps of a) providing a detection apparatus comprising(i) a movable light coupler, (ii) a waveguide comprising a core layerand a first cladding layer, wherein at least one adapter site for themovable light coupler is formed in at least the first cladding layer,and (iii) a light detector; b) providing at least one nucleic acidmolecule; c) localizing the at least one nucleic acid moleculeindividually on the movable light coupler; d) localizing at the adaptersite the movable light coupler on which at least one nucleic acid islocalized; e) performing single molecule sequencing-by-synthesis of theat least one nucleic acid molecule, wherein the single molecule nucleicacid sequencing-by-synthesis produces an emitted light correlated to theidentity of at least one base in the nucleic acid; f) detecting theemitted light with the detector, resulting in an output signal; and g)processing the output signal to determine an identity of at least onebase comprised by the nucleic acid.

In some embodiments, the methods comprise forming covalent attachments,such as between reagents or target objects and labels and betweenfunctional groups and surfaces, e.g., surfaces of a movable lightcoupler or of the adapter site. For example, to prepare movable lightcoupler particles modified with oligonucleotides, streptavidin may belinked to the surface of a light coupler in order to bind biotinylatedoligonucleotides. In some embodiments, a single-molecule object bindingmoiety such as a polypeptide or polypeptide complex may be linked to thesurface of a light coupler. Many methods for forming covalentattachments, such as of reagents to surfaces or labels, are known in theart. Non-covalent attachment methods can also be used. A number ofdifferent chemical modifiers can be used to facilitate attachmentformation. Examples of chemical modifiers include N-hydroxy succinimide(NHS) groups, amines, aldehydes, epoxides, carboxyl groups, hydroxylgroups, hydrazides, hydrophobic groups, membranes, maleimides, biotin,streptavidin, thiol groups, nickel chelates, photoreactive groups, borongroups, thioesters, cysteines, disulfide groups, alkyl and acyl halidegroups, glutathiones, maltoses, azides, phosphates, and phosphines.These can easily be prepared, for example, using standard methods(MICROARRAY BIOCHIP TECHNOLOGIES, Mark Schena, Editor, March 2000,Biotechniques Books). In some embodiments, attachments are formedbetween two entities by using an appropriate combination of modifiers(e.g., an electrophilic modifier and a nucleophilic modifier), whereineach entity comprises at least one modifier.

In some embodiments, attachments are formed between two entities byusing a chemical modifier present on one of the entities and anaturally-occurring moiety, for example, an amine or sulfhydryl, of theother entity. In some embodiments, modifiers that are reactive to aminesare used. An advantage of this reaction is that it can be fast and canavoid production of toxic by-products. Examples of such modifiersinclude NHS-esters, aldehydes, epoxides, acyl halides, and thio-esters.Most proteins, peptides, glycopeptides, etc., have free amine groups,which can react with such modifiers to link them covalently to thesemodifiers. Nucleic acid probes with internal or terminal amine groupscan also be synthesized, and are commercially available (e.g., from IDTor Operon). Thus, biomolecules can be bound (e.g., covalently ornon-covalently) to labels, surfaces, or other reagents using similarchemistries.

A number of other multi-functional cross-linking agents can be used toconvert the chemical reactivity of one kind of modifier to another.These groups can be bifunctional, tri-functional, tetra-functional, andso on. They can also be homo-functional or hetero-functional. An exampleof a bi-functional cross-linker is X—Y—Z, where X and Z are two reactivegroups, and Y is a connecting linker. Further, if X and Z are the samegroup, such as NHS-esters, the resulting cross-linker, NHS—Y—NHS, is ahomo-bi-functional cross-linker and could connect two entities that eachcomprise an amine. If X is NHS-ester and Z is a maleimide group, theresulting cross-linker, NHS—Y-maleimide, is a hetero-bi-functionalcross-linker and could link an entity comprising an amine with an entitycomprising a thio-group. Cross-linkers with a number of differentfunctional groups are widely available. Examples of such functionalgroups include NHS-esters, thio-esters, alkyl halides, acyl halides(e.g., iodoacetamide), thiols, amines, cysteines, histidines,di-sulfides, maleimide, cis-diols, boronic acid, hydroxamic acid,azides, hydrazines, phosphines, photoreactive groups (e.g.,anthraquinone, benzophenone), acrylamide (e.g., acrydite), affinitygroups (e.g., biotin, streptavidin, maltose, maltose binding protein,glutathione, glutathione-S-transferase), aldehydes, ketones, carboxylicacids, phosphates, hydrophobic groups (e.g., phenyl, cholesterol), etc.

Other modifier alternatives (such as photo-crosslinking and thermalcrosslinking) are known to those skilled in the art. Commerciallyavailable technologies include, for example, those from MosiacTechnologies (Waltham, Mass.), EXIQON™ (Vedbaek, Denmark), Schleicherand Schuell (Keene, N. H.), Surmodics™ (St. Paul, Minn.), XENOPORE™(Hawthorne, N. J.), Pamgene (Netherlands), Eppendorf (Germany), Prolinx(Bothell, Wash.), Spectral Genomics (Houston, Tex.), and COMBIMATRIX™(Bothell, Wash.).

2.1 Labels for Use with the Detection System

In some embodiments of the methods described herein, one or more labelsare attached to the target single-molecule object(s) (i.e., thesubstance[s] to be detected, such as nucleotides, including nucleotideanalogs), or to the probe(s), such as primers, antibodies, or otherreagents that interact with the object(s) or other reagent(s). Any labelcan be used on the single-molecule object or probe which can be usefulin the correlation of signal with the amount or presence of the object.

For example, a wide variety of fluorescent molecules can be utilized,including small molecules, fluorescent proteins, and quantum dots.Useful fluorescent molecules (fluorophores) include, but are not limitedto: 1,5 IAEDANS; 1,8-ANS; 4-Methylumbelliferone;5-carboxy-2,7-dichlorofluorescein; 5-Carboxyfluorescein (5-FAM);5-Carboxynapthofluorescein; 5-Carboxytetramethylrhodamine(5-TAMRA);5-FAM (5-Carboxyfluorescein); 5-HAT (Hydroxy Tryptamine); 5-HydroxyTryptamine (HAT); 5-ROX (carboxy-X-rhodamine); 5-TAMRA(5-Carboxytetramethylrhodamine); 6-Carboxyrhodamine 6G; 6-CR 6G; 6-JOE;7-Amino-4-methylcoumarin; 7-Aminoactinomycin D (7-AAD);7-Hydroxy-4-methylcoumarin; 9-Amino-6-chloro-2-methoxyacridine; ABQ;Acid Fuchsin; ACMA (9-Amino-6-chloro-2-methoxyacridine); AcridineOrange; Acridine Red; Acridine Yellow; Acriflavin; Acriflavin FeulgenSITSA; AFPs-AutoFluorescent Protein-(Quantum Biotechnologies); TexasRed; Texas Red-X conjugate; Thiadicarbocyanine (DiSC3); Thiazine Red R;Thiazole Orange; Thioflavin 5; Thioflavin S; Thioflavin TCN; Thiolyte;Thiozole Orange; Tinopol CBS (Calcofluor White); TMR; TO-PRO-1;TO-PRO-3; TO-PRO-5; TOTO-1; TOTO-3; TriColor (PE-Cy5); TRITC(TetramethylRodaminelsoThioCyanate); True Blue; TruRed; Ultralite;Uranine B; Uvitex SFC; WW 781; X-Rhodamine; XRITC; Xylene Orange; Y66F;Y66H; Y66W; YO-PRO-1; YO-PRO-3; YOYO-1; interchelating dyes such asYOYO-3, Sybr Green, Thiazole orange; members of the Alexa Fluor dyeseries (from Molecular Probes/Invitrogen) which cover a broad spectrumand match the principal output wavelengths of common excitation sourcessuch as Alexa Fluor 350, Alexa Fluor 405, 430, 488, 500, 514, 532, 546,555, 568, 594, 610, 633, 635, 647, 660, 680, 700, and 750; members ofthe Cy Dye fluorophore series (GE Healthcare), also covering a widespectrum such as Cy3, Cy3B, Cy3.5, Cy5, Cy5.5, Cy7; members of theOyster dye fluorophores (Denovo Biolabels) such as Oyster-500, -550,-556, 645, 650, 656; members of the DY-Labels series (Dyomics), forexample, with maxima of absorption that range from 418 nm (DY-415) to844 nm (DY-831) such as DY-415, -495, -505, -547, -548, -549, -550,-554, -555, -556, -560, -590, -610, -615, -630, -631, -632, -633, -634,-635, -636, -647, -648, -649, -650, -651, -652, -675, -676, -677, -680,681, -682, -700, -701, -730, -731, -732, -734, -750, -751, -752, -776,-780, -781, -782, -831, -480XL, -481XL, -485XL, -510XL, -520XL, -521XL;members of the ATTO series of fluorescent labels (ATTO-TEC GmbH) such asATTO 390, 425, 465, 488, 495, 520, 532, 550, 565, 590, 594, 610, 611×,620, 633, 635, 637, 647, 647N, 655, 680, 700, 725, 740; members of theCAL Fluor series or Quasar series of dyes (Biosearch Technologies) suchas CAL Fluor Gold 540, CAL Fluor Orange 560, Quasar 570, CAL Fluor Red590, CAL Fluor Red 610, CAL Fluor Red 635, Quasar 670; quantum dots,such as quantum dots of the EviTags series (Evident Technologies) orquantum dots of the Qdot series (Invitrogen) such as the Qdot 525,Qdot565, Qdot585, Qdot605, Qdot655, Qdot705, Qdot 800; fluorescein;rhodamine; and/or phycoerythrin; or combinations thereof. See, e.g.,U.S. Application Publication No. 2008/0081769.

In embodiments encompassing single-molecule nucleic acid sequencing of atarget nucleic acid localized on a movable light coupler which islocalized at an adapter site, nucleotides incorporated into a nascentDNA strand may be detected by excitation and detection of a fluorophorelinked directly to the incoming nucleotide, e.g., a fluorophore that islinked to the beta or gamma phosphate of the dNTP and that is cleavedupon incorporation of the dNTP into the growing strand. In someembodiments, nucleotides incorporated into a nascent strand are detectedusing fluorescence resonance energy transfer (FRET)-based detection. Forexample, in some embodiments, a FRET-based method as described in U.S.Patent Application No. 2010/0035268 can be used. In such embodiments, aQuantum dot capable of acting as a fluorescence donor may be linked to asequencing primer, and the dNTPs used to synthesize the growing strandcarry a fluorescence acceptor group on their terminal (gamma) phosphategroup. Incorporation of the fluorophore-labeled nucleotidepolyphosphates into the growing nucleotide strand at an active sitecomplementary to the target nucleic acid is detected in real-time bydetecting emission of the dNTP-linked fluorescence acceptors followingfluorescence resonance energy transfer from the excited Quantum dotfluorescence donor. The identity of each incorporated nucleotide isdetermined by its fluorescent label, wherein the fluorescence label isthen cleaved from the nucleotide upon incorporation into the growingstrand.

2.2 Nucleic Acid Detection

The detection system may be used in methods or processes of moleculedetection, e.g., nucleic acid sequencing. This system, and methods orprocesses utilizing it, are useful for, e.g., analytical and diagnosticapplications.

The detection system may be used with a wide variety of sequencingmodalities and may be suitable for sequencing single molecules.Additionally, the detection system has simplified design, assembly, andproduction relative to existing biochip devices.

2.2.1 Molecules to be Detected

Nucleic acids suitable for detection may include any nucleic acid,including, for example, DNA, RNA, or PNA (peptide nucleic acid), and maycontain any sequence—both known and unknown, including naturallyoccurring or artificial sequences. The nucleic acid may be naturallyderived, recombinantly produced, or chemically synthesized. The nucleicacid may comprise naturally-occurring nucleotides, nucleotide analogsnot existing in nature, or modified nucleotides. The length of thenucleic acid to be detected may vary based on the actual application. Insome embodiments, the nucleic acid may include at least 10, 20, 50, 100,200, 500, 1000, 2000, 5000, 10000, 20000 bases, or more. In someembodiments, the nucleic acid may be from 10 to 20, from 10 to 50, from10 to 100, from 50 to 100, from 50 to 500, from 50 to 1000, from 50 to5000, from 500 to 2000, from 500 to 5000, or from 1000 to 5000 bases.

A nucleic acid may be single-stranded for detection. Single strandednucleic acid templates may be derived from a double stranded molecule bymeans known in the art including, for example, heating or alkali orother chemical treatment. Single stranded nucleic acid templates mayalso be produced by, e.g., chemical or in vitro synthesis.

In some embodiments, the nucleic acid to be detected is circular. Insome embodiments, the methods comprise providing a circular nucleic acidmolecule comprising an insert with a known sequence, which can be usedas a binding site for a primer. The circular nucleic acid molecule canbe provided in a single- or double-stranded state, and will generallycomprise at least one covalently closed strand. Double-stranded circularmolecules may comprise a nicked strand or a second covalently closedstrand.

In some embodiments, the circular nucleic acid molecule is provided byisolating it in circular form from its source, if part of its sequenceis known and thus can serve as the nucleic acid insert (e.g., aconserved motif within the sequence of a gene contained in the circularmolecule may be known, or the molecule may be known to contain asequence based on its ability to hybridize under high stringencyconditions to another nucleic acid of known sequence). In someembodiments, the sequence of the nucleic acid insert is known onlyinexactly, as would be the case when knowledge of the sequence isderived from stringent hybridization properties. In some embodiments,the sequence of the nucleic acid insert is known exactly, such as wouldbe the case when the circular nucleic acid molecule has a known backbonesequence or has been engineered to contain a known sequence.

In some embodiments, the circular nucleic acid molecule is provided byperforming an in vitro reaction or reactions to incorporate a linearnucleic acid sample into a circular molecule along with a nucleic acidinsert. The in vitro reaction or reactions can in some embodimentscomprise ligation by a ligase and/or other strand joining reactions suchas can be catalyzed by various enzymes, including recombinases andtopoisomerases. DNA ligase or RNA ligase may be used to enzymaticallyjoin the two ends of a linear template, with or without an adaptermolecule or linkers, to form a circle, as exemplified in FIG. 8. Forexample, T4 RNA ligase couples single-stranded DNA or RNA, as describedin Tessier et al., ANAL BIOCHEM, 158: 171-78 (1986). CIRCLIGASE™(Epicentre, Madison, Wis.) may also be used to catalyze the ligation ofa single stranded nucleic acid. Alternatively, a double stranded ligase,such as E. coli or T4 DNA ligase, may be used to perform thecircularization reaction.

In some embodiments, providing the circular nucleic acid moleculecomprises replicating a nucleic acid template by extending from at leastone primer (which can include random primers with 5′ flaps of knownsequence that can serve as the nucleic acid insert) comprisingcomplementary regions and circularizing the amplified nucleic acid, suchas may be catalyzed by a ligase or a recombinase; the amplified nucleicacid may in some embodiments be processed at its ends, e.g., byrestriction or phosphorylation, prior to circularization.

In some embodiments, the circular nucleic acid molecule is provided byperforming chemical circularization. Chemical methods employ knowncoupling agents such as BrCN plus imidazole and a divalent metal,N-cyanoimidazole with ZnCl₂,1-(3-dimethylaminopropyl)-3ethylcarbodiimide HCl, and other carbodiimides and carbonyldiimidazoles. The ends of a linear template may also be joined bycondensing a 5′-phosphate and a 3′-hydroxyl, or a 5′-hydroxyl and a3′-phosphate.

In some embodiments, the circular nucleic acid molecule contains aninsert sequence that could be considered an end link primer (discussedbelow) except that it is not at an end, since the molecule is circular.

2.2.1.1 End Link Primer

In some embodiments, a linear nucleic acid may further comprise one ormore end link primers coupled to the 5′ end, the 3′ end, or both the 5′end and the 3′ end of the nucleic acid. In particular embodiments, anend link primer may be affixed to the 3′ end of the nucleic acid. Endlink primers may be used to provide a complementary sequence for one ormore detecting primers, e.g., a sequencing primer.

End link primers are short nucleic acid molecules usually composed ofless than 100 nucleotides. In some embodiments, the end link primer maybe at least 5, 10, 15, 20, 25, 30, 50, 75, 90 nucleotides, or more, inlength. In certain embodiments, end link primers may be from 8 to 25,from 10 to 20, from 10 to 30, or from 10 to 50 nucleotides in length. Insome embodiments, the end link primers may be unbranched, however, inother embodiments, they may be branched.

The end link primer may serve as a complement to one or more primersused to detect the nucleic acid, e.g., a sequencing primer. In someembodiments, the primer may be used to detect the nucleic acid byhybridization, e.g., the primer may contain a detectable label, e.g., afluorescent label. In some embodiments, the 5′ end of the end linkprimer may comprise a sequence complementary to a sequencing primer. Insome embodiments, the end link primer sequence that is complementary tothe sequencing primer may be oriented so that the 3′ end of thesequencing primer may be immediately adjacent to the first nucleotide inthe nucleic acid to be sequenced.

In some embodiments, end link primers may be added to ends of thenucleic acid to be detected by a ligase, for example, a DNA ligase. Insome embodiments, the end link primer and nucleic acid to be detectedmay be both single stranded before the ligation. In other embodiments,both may be double stranded. In still other embodiments, one may besingle stranded and the other may be double stranded. Ligation is wellknown in the art. For example, in the polony sequencing method, Shendureet al. (SCIENCE, 309:1728-1732 [2005]) ligated a T30 end link primer (32bp) to a sample DNA segment with the New England Biolabs' (NEB) QuickLigation™ kit. There, the ligation reaction solution included 0.26 pmoleof DNA, 0.8 pmole of T30 end link primer, 4.0 μl T4 DNA Ligase, in 1×Quick Ligation Buffer. After mixing, the reaction solution was incubatedfor about 10 minutes at room temperature, and then placed on ice. Theligation reaction was stopped by heating the samples to 65° C. for 10minutes.

In other embodiments, the end link primer may be synthesized on thenucleic acid to be sequenced. For example, the end link primer may be ahomopolymer added by, e.g., terminal transferase. For example, Harris etal., (SCIENCE 320:106-109 [2008]) added a poly-A tail to DNA templates,which served as the complement to a poly-T sequencing primer in thesingle molecule sequencing of a viral genome.

2.2.1.2 Sequencing Primer

A sequencing primer is a single-stranded oligonucleotide complementaryto a segment of the nucleic acid to be detected or its associated endlink primer. In some embodiments, the sequencing primer may be at least8, 10, 15, 20, 25, 30, 35, 40, 45, 50 nucleotides, or more in length. Inparticular embodiments, the sequencing primer may be from 8 to 25, from10 to 20, from 10 to 30, or from 10 to 50 nucleotides in length. Thesequencing primer may be made up of any type of nucleotide, includingnaturally-occurring nucleotides, nucleotide analogs not existing innature, or modified nucleotides.

In some embodiments, a sequencing primer may contain modifiednucleotides, e.g., locked nucleic acids (LNAs; modified ribonucleotides,which provide enhanced base stacking interactions in a polynucleicacid). As an illustration of the utility of LNAs, Levin et al. (NUCLEICACID RESEARCH 34(20):142 [2006]) showed that a LNA-containing primer hadimproved specificity and exhibited stronger binding relative to thecorresponding unlocked primer. Three variants of the MCP1 primer(5′-cttaaattttcttgaat-3′) containing 3 LNA nucleotides (in caps) atdifferent positions in the primer were made: MCP1-LNA-3′(5′-cttaaattttCtTgaAt-3′); MCP1-LNA-5′ (5′-CtTaAattttcttgaat-3′); andMCP1-LNA-even (5′-ctTaaatTttctTgaat-3′). All LNA-substituted primers hadenhanced T_(m), while the MCP1-LNA-5′ primer exhibited particularlyenhanced sequencing accuracy (Phred Q30 counts). Accordingly, inparticular embodiments, the sequencing primer may contain at least onelocked nucleotide in its 5′ region, i.e., the 5′ half, third, or quarterof the sequencing primer.

Sequencing primers and single-stranded target nucleic acids (i.e., anucleic acid to be sequenced including at least one end link primer) maybe hybridized before or after being combined with a nucleic acidpolymerizing enzyme, dNTPs, and appropriate buffer components fornucleic acid polymerization, and may then be adsorbed to a movable lightcoupler. The sequencing primer and sample nucleic acid may be hybridizedby mixing the sample nucleic acid with a molar excess of sequencingprimer in a salt-containing solution, such as 5×SSC (or 5×SSPE), 0.1%Tween 20 (or 0.1% SDS), and 0.1% BSA buffer. The mixture may be heatedto 65° C. for at least 5 minutes and slowly cooled to room temperature,to allow primer/template annealing. Residual primers may be eliminatedby appropriate means including, e.g., a molecular sieve.

In some embodiments, a target nucleic acid is localized on a movablelight coupler as a component of a nucleic acid-synthesizing reactioncomplex, wherein neither the synthesis reaction may be localized in aconfined space at a waveguide adapter site without requiringimmobilization of the polymerase or target nucleic acid to a surface. Toprepare a nucleic-acid synthesizing reaction complex localized on thesurface of movable light coupler, a circularized target nucleic acidprepared as described may be combined with a sequencing primer, anucleic acid polymerizing enzyme, dNTPs, and appropriate buffercomponents for nucleic acid synthesis. The polymerase may proceed aroundthe circularized template in multiple cycles, generating a growingnascent strand comprising multiple copies of the template strand. Thepolymerizing complex may then be combined with a movable light couplermodified with oligonucleotides on its surface, as shown schematically inFIG. 9. Thus, in such embodiments, neither the target strand templatenor the polymerase is itself immobilzed on a surface. Theoligonucleotides may comprise a sequence that hybridizes to thesequencing primer sequence, multiple copies of which may be embedded inthe growing nascent strand. These embedded sequences may bind to theoligonucleotides bound to the surface of the light coupler, as shownschematically in FIG. 10. In some embodiments, the oligonucleotidescomprise random sequences, which may hybridize to the growing nascentstrand in various locations, as shown schematically in FIG. 11. In someembodiments, the movable light coupler may is modified witholigonucleotides over its entire surface, as shown in FIG. 9. In furtherembodiments, the movable light coupler is modified with oligonucleotideson only a portion of its surface, as shown in FIG. 10 and FIG. 11.

In some embodiments, a double-stranded target sequence comprising astrand with incorporated biotinylated uracil bases is generated bypreparing a circular, single-stranded target strand using a linkingprimer which is able to hybridize to both ends of the single-strandedtarget nucleic acid, and polymerizing a second strand with a nucleicacid polymerase and a dNTP mixture supplemented with biotinylated dUTP,as shown in FIG. 12. The double-stranded target may be denatured andcombined with streptavidin-modified light coupler particles, therebyadsorbing the denatured target strand to the light coupler by virtue ofthe biotinylated strand with which it is intertwined, as shown in FIG.13A. Upon addition of a polymerase, dNTPs, a sequencing primer, andappropriate buffer components for nucleic acid synthesis, a nucleicacid-synthesizing reaction complex may form, wherein the complex isadsorbed to the surface of a movable light coupler withoutimmobilization of the polymerase or the target nucleic acid, as shown inFIGS. 13B and 13C. A polymerase, dNTPs, and buffer components can beadded before or after localization of the light coupler with adsorbedtemplate at adapter site.

Primers, including both end link and sequencing primers, may be designedby appropriate means, including visual inspection of the sequence orcomputer-assisted primer design. Numerous software packages areavailable to assist in the primer design, including DNAStar™ (DNAStar,Inc., Madison, Wis.), OLIGO 4.0 (National Biosciences, Inc.), VectorNTI® (Invitrogen), Primer Premier 5 (Premierbiosoft), and Primer3(Whitehead Institute for Biomedical Research, Cambridge, Mass.). Primersmay be designed taking into account, for example, the molecule to besequenced, specificity, length, desired melting temperature, secondarystructure, primer dimers, GC content, pH and ionic strength of thebuffer solution, and the enzyme used (i.e., polymerase or ligase). See,e.g., Joseph Sambrook and David Russell, MOLECULAR CLONING: A LABORATORYMANUAL Cold Spring Harbor Laboratory Press; 3rd edition (2001).

2.2.2 Sequencing Modalities

Some embodiments are methods of sequencing a nucleic acid, comprisingthe steps of a) providing a detection apparatus comprising (i) a movablelight coupler, (ii) a waveguide comprising a core layer and a firstcladding layer, wherein at least one adapter site for the movable lightcoupler is formed in at least the first cladding layer, and (iii) alight detector; b) providing at least one nucleic acid molecule; c)localizing the at least one nucleic acid molecule individually on thesurface of the movable light coupler; d) localizing at the adapter sitethe movable light coupler having the at least one nucleic acid localizedon its surface; e) performing single molecule sequencing-by-synthesis ofthe at least one nucleic acid molecule, wherein the single moleculenucleic acid sequencing-by-synthesis leads to emission of lightcorrelated to the identity of at least one base in the nucleic acid; f)detecting the light with the detector, resulting in an output signal;and g) processing the output signal to determine an identity of at leastone base comprised by the nucleic acid.

In these methods, “localizing the at least one nucleic acid moleculeindividually on the surface of the movable light coupler and localizingat the adapter site the movable light coupler having the at least onenucleic acid localized on its surface” is understood to mean that asingle nucleic acid molecule may be located on a movable light couplerwhich is localized at an adapter site, i.e., there is at least oneadapter site in which one (and not more than one) nucleic acid moleculeis localized. In some embodiments, there are a plurality of adaptersites which each individually contain one (and not more than one)movable light coupler comprising a nucleic acid molecule localized onits surface. In some embodiments, during operation, some of theplurality of adapter sites contain light couplers each having one targetnucleic acid molecule localized on its surface, and other adapter siteseither do not contain light couplers or contain light couplers that donot have a surface-localized target nucleic acid molecule. That is, theconcentration of light couplers with surface-localized nucleic acids inthe sample solution is lower than a certain value so that not alladapter sites have light couplers with surface-localized nucleic acidcontained in them. This may prevent the scenario that two or morenucleic acid molecules localize at an adapter site before a sequencingis completed, so as to prevent the results of one sequencing fromcomprising information from more than one molecule. For example, in someembodiments, less than or equal to 50%, 40%, 30%, 25%, 20%, 15%, 10%,9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% of the adapter sites will generatea signal due to the low concentration of the biological moleculeslocalized at adapter sites to be detected or identified. In instances inwhich a first target nucleic acid dissociates from the surface of alight coupler localized at an adapter site, and a second nucleic acidsubsequently associates with the same light coupler localized at theadapter site, the results of sequencing the first nucleic acid may bedistinguished from the results of sequencing of the second nucleic acidby any gap in the detection of incorporated nucleotides and/or bydifferences in the determined nucleotide sequences.

In some embodiments, the single molecule nucleic acidsequencing-by-synthesis leads to emission of light viachemiluminescence. Notably, in these embodiments, it is not necessaryfor the apparatus to comprise a light source, as chemiluminescencegenerates light from chemical energy.

In some embodiments, the apparatus further comprises a light source,which may be used to provide excitatory light, e.g., for causing thesingle molecule nucleic acid sequencing-by-synthesis to emit light viafluorescence.

The detection apparatuses and methods may be used to detect and sequencenucleic acids by means known in the art, as reviewed in, e.g., U.S. Pat.No. 6,946,249 and Shendure et al., NAT. REV. GENET. 5:335-44 (2004). Thesequence modalities can be chosen from single-molecule sequencingmethods known in the art. In some embodiments, the sequencing methodsmay rely on the specificity of either a DNA polymerase or DNA ligase andmay include, e.g., base extension sequencing (single base stepwiseextensions) and multi-base sequencing-by-synthesis (including, e.g.,sequencing with terminally-labeled nucleotides).

For single-molecule sequencing modalities, the detection system canoffer the advantage of being able to resequence single molecules. Forexample, a template nucleic acid molecule to be sequenced can beprovided in circular form together with a sequencing primer.Resequencing can be achieved by performing a plurality of sequencingcycles such that a sequence read is obtained that is greater than thenumber of nucleotides in the template nucleic acid molecule. Thesequencing read therefore comprises information that redundantlyidentifies the base in at least one position in the template nucleicacid molecule. In some embodiments, the sequencing read comprisesinformation that redundantly identifies at least 25%, 50%, 75%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the bases in thetemplate nucleic acid molecule. In some embodiments, the sequencing readcomprises information that identifies at least 25%, 50%, 75%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the bases in thetemplate nucleic acid molecule with three-fold, four-fold, five-fold,seven-fold, or ten-fold or greater redundancy. By resequencing the samemolecule, sequencing errors are expected to fall as the power of thenumber of sequencing reads. For example, if per base error rates for asingle read are 10⁻³, then after two reads, this falls to (10⁻³)², i.e.,10⁻⁶. This is particularly advantageous for single-molecule sequencingsince the modified nucleotides used for sequencing can lose their labelsor blocking groups resulting in, e.g., spurious deletions.

The viability of enzymes and fluorophore labels on nucleotides can begradually lost as a nucleic acid synthesis reaction proceeds. When therate of sequence reading slows down, a reaction mixture can be washedout of the detection system and replaced with fresh solutions forcontinuous sequence reading. In some embodiments, the reaction mixtureis supplemented with fresh reagents rather than washed out and replaced.

In general, in single-molecule sequencing, at least one nucleic acidmolecule to be sequenced is contacted with a primer. The primer ismodified, e.g., by performing at least one enzyme-catalyzedpolymerization or ligation reaction. The at least one reaction leads toemission of light correlated to the identity of at least one base in thenucleic acid. “Leading to” emission of light is understood to mean thatthe at least one reaction causes at least one condition under whichlight emission correlated to the identity of at least one base in thenucleic acid occurs; this occurrence may be via interaction withexcitatory light, a chemi- or bio-luminescent system, etc. The at leastone condition can be, for example, incorporation of a fluorophore intothe product of the at least one reaction, or the release ofpyrophosphate. Thus, light may be generated with or without externalexcitation. For example, single-molecule sequencing can be performedwith reversible terminator base analogs comprising a covalently-linkeddetectable label, e.g., a fluorescent label, and a blocking group toprevent any secondary extension, wherein the analog is excited anddetected after it has been added to the primer, and the label andblocking group are removed after addition to allow another round ofextension. Alternatively, a product of an extension step, such as apyrophosphate, can be detected without external excitation by providinga chemi- or bio-luminescent detection system which emits light in apyrophosphate-dependent manner. These and other modalities are discussedin more detail below.

The light emitted is correlated to the identity of at least one base inthe nucleic acid. In some embodiments, the correlation can be temporal;e.g., the time of emission of the light indicates the identity of the atleast one base, such as is the case when different base analogs areprovided for use in a polymerization reaction at different times. Insome embodiments, the correlation can be spectral; e.g., the spectrum ofthe emitted light indicates the identity of the at least one base, suchas is the case when different base analogs that comprise differentfluorophores are provided for use in a polymerization reaction.

In some embodiments, single-molecule nucleic acid sequencing comprisesmultiple sequencing cycles. A sequencing cycle is understood to mean theevents that lead to an emission of light correlated to the identity ofat least one base that would be repeated in order to identify at least asecond base in the nucleic acid after a first base has been identified.Thus, in methods that comprise single-molecule nucleic acid sequencing,the single-molecule nucleic acid sequencing can comprise at least agiven number of sequencing cycles that lead to at least the given numberof emissions of light correlated collectively to the identity of atleast the given number of bases in the nucleic acid, and the methodcomprises identifying at least the given number of bases in the nucleicacid. In some embodiments, the given number may be, for example, 2, 3,4, 5, 10, 20, 50, 100, 200, or 500.

Sequencing methods can comprise determining the identity of one or morebases in a nucleic acid. In some embodiments in which performingsingle-molecule nucleic acid sequencing leads to emission of light thatis detected with at least one light detector comprising at least a firstoptical sensor and a second optical sensor, and output signal from theat least two optical sensors is processed, the identity of at least onebase in a nucleic acid can be determined by comparing at least oneresult of the processing with at least one known result corresponding toat least one known type.

For example, a result of the processing can indicate a time at which areaction occurred; when light emitted is temporally correlated to theidentity of at least one base in the nucleic acid, said time can be usedto identify at least one base in the nucleic acid.

In another example, a result of the processing can be a determination ofwhich fluorophore was incorporated into the product of a reaction; whenlight emitted is spectrally correlated to the identity of at least onebase in the nucleic acid, said determination can be used to identify atleast one base in the nucleic acid.

2.2.2.1 Base Extension Sequencing: Stepwise Extension

In some embodiments, a detection system may be used to detect lightgenerated during base extension sequencing. In some embodiments, baseextension sequencing begins by providing a partial duplex sample nucleicacid comprising a single-stranded nucleic acid to be sequenced, an endlink primer associated with the 3′ end of nucleic acid to be sequenced,and a sequencing primer annealed thereto. In some embodiments,polymerase and modified nucleotides may be then applied to the lightdetection system in a suitable buffer. In some embodiments, thenucleotides may include a covalently-linked detectable label, e.g., afluorescent label, and a blocking group to prevent any secondaryextension. Accordingly, the sequencing pauses after the addition of asingle nucleotide to the 3′ end of sequencing primer.

In a first step of one embodiment of a base extension sequencingreaction, a nucleotide with a fluorescent blocking group may be added bya DNA polymerase to the 3′ end of sequencing primer. In someembodiments, the fluorescent label may act as the blocking group. Inother embodiments, they may be separate moieties. A single nucleotidemay be incorporated at the 3′ end of sequencing primer and is identifiedby its label by the corresponding light detector. The fluorescent labeland blocking group are then removed, e.g., by chemical or enzymaticlysis, to permit additional cycles of base extension. In certainembodiments, the label and blocking groups may be removed simultaneouslyor sequentially and in any order. By compiling the order of the basesadded, the sequence of the sample nucleic acid may be deduced in the 3′to 5′ direction, one base at a time.

Generally, there are two ways to recognize the nucleotide added duringstepwise extension. In the first case, the four nucleotides may all havethe same detectable label, but are added one at a time, in apredetermined order. The identity of the extended nucleotide may bedetermined by the order that the nucleotide is added in the extensionreaction. In the second mode for recognizing the base integrated duringextension, four different nucleotides may be added at the same time andeach is coupled with a distinct detectable label. In differentembodiments, the excitation or emission spectra and/or intensity of thelabels may differ. The identity of the nucleotide added in the extensionmay be determined by the intensity and/or wavelength (i.e., excitationor emission spectra) of the detected label.

2.2.2.2 Sequencing by Synthesis: Multi-Step Extension

In some embodiments, sequencing by synthesis may proceed with multipleuninterrupted extensions, e.g., without the use of blocking groups. Inthese embodiments, the polymerization reaction may be monitored bydetecting the release of the pyrophosphate after nucleoside triphosphatehydrolysis, i.e., the release of the beta and gamma phosphate complex.This complex may be detected directly, for example, by a fluorescentmoiety on the complex, or indirectly, for example, by coupling thepyrophosphate to a chemi- or bio-luminescent detection system, asdiscussed above.

In some embodiments, the sample nucleic acid may be sequencedessentially continuously by using terminal-phosphate-labelednucleotides. Exemplary embodiments of terminal-phosphate-labelednucleotides and methods of their use are described in, e.g., U.S. Pat.No. 7,361,466 and U.S. Patent Publication No. 2007/0141598, publishedJun. 21, 2007. Briefly, the nucleotides may be applied to the detectionsystem and, when hydrolyzed during the polymerization, the labeledpyrophosphate may be detected by a corresponding light detector. In someembodiments, all four nucleotides may comprise distinct labels and beadded simultaneously. In some embodiments, the nucleotides may compriseindistinguishable, e.g., identical, labels and be added sequentially ina predetermined order. Sequential, cyclical addition of nucleotides withindistinguishable labels still permits multiple, uninterruptedpolymerization steps, e.g., in homopolymer sequences.

2.2.3 Additional Applications

The detection apparatus may simultaneously detect millions of nucleicacid segments. If each segment is, for example, 1000 bases long, asingle device could obtain upwards of billions of base sequences atonce. Discussed below are additional applications of the systems andmethods provided herein.

2.2.3.1 Whole-Genome Sequencing

The detection system may be used to perform whole or partial genomesequencing of, e.g., a virus, bacterium, fungi, eukaryote, orvertebrate, e.g., a mammal, e.g., a human.

Genomic DNA may be sheared into fragments of at least 20, 50, 100, 200,300, 500, 800, 1200, 1500 nucleotides, or longer, for sequencing. Insome embodiments, the sheared genomic DNA may be from 20 to 50, from 20to 100, from 20 to 500, from 20 to 1000, from 500 to 1200, or from 500to 1500 nucleotides long. In some embodiments, the nucleic acids to besequenced, along with associated end link primers, may be made singlestranded, annealed to a sequencing primer, and applied to the detectionsystem for sequencing as described above.

2.2.3.2 Gene Expression Profiling

In other embodiments, the detection system may be used to sequence cDNAfor gene expression profiling. For example, mRNA levels may bequantified by measuring the relative frequency that a particularsequence is detected on a device. Several million cDNA molecules may besequenced in parallel on a device as described herein. If a cellcontains, on average, 350,000 mRNA molecules, a transcript present ateven one copy per cell is expected to be sequenced approximately threetimes in one million sequencing reactions. Accordingly, the detectionsystem is suitable for single-molecule sequencing withsingle-copy-number sensitivity. In other embodiments, the detectionsystem may be used to sequence RNA directly for gene expressionprofiling (, i.e., direct RNA sequencing, see e.g., Ozsolak et al.,NATURE 461: 814-818 (2009)).

cDNA synthesis is well known in the art and typically includes total RNAextraction with optional enrichment of mRNA. cDNA is produced from mRNAby steps including, for example: reverse transcription, for first strandsynthesis; RNAse treatment, to remove residual RNA; random hexamerpriming of the first strand, and second strand synthesis by DNApolymerase. The resultant cDNA is suitable for sequencing on the systemsdescribed herein. Methods of isolating and preparing both DNA and RNAare well known in the art. See, for example, Joseph Sambrook and DavidRussell, MOLECULAR CLONING: A LABORATORY MANUAL Cold Spring HarborLaboratory Press; 3rd edition (2001).

2.2.3.3 Additional Detection Methods

(a) FRET

In some embodiments, a molecule may be detected on the detection systemby fluorescence resonance energy transfer (FRET; also known as Försterresonance energy transfer). As is known in the art, FRET occurs when anexcited donor molecule non-radiatively transfers energy to an acceptormolecule, which emits the energy, typically as light. FRET can helpreduce background light by, e.g., providing greater spectral separationbetween effective excitation and emission wavelengths for a moleculebeing detected. FRET is often used to detect close molecularinteractions since its efficiency decays as the sixth power of thedistance between donor and acceptor molecules. For example, Zhang et al.(NATURE MATERIALS 4:826-31 [2005]) detected nucleic acid hybridizationby FRET. There, a biotinylated nucleic acid target was conjugated to anavidin-coated quantum dot donor, which then excited a Cy5-conjugated DNAprobe. In some embodiments, a labeled molecule free in a sample solutionand a labeled molecule or molecular complex which binds to the freemolecule and is localized on the surface of a movable light coupler mayform a donor/acceptor (or vice versa) pair for detection by FRET.

In some embodiments of nucleic acid sequencing using the detectionsystem, fluorescently labeled nucleotides may act as acceptorchromophores for a donor chromophore attached to a polymerase or ligase.Accordingly, in these embodiments, the donor chromophore located on thepolymerase or ligase may excite an acceptor chromophore on a nucleotidebeing polymerized on, or ligated to, the target nucleic acid.Nucleotides not proximate to the polymerase may be not excited due tothe rapid falloff in FRET efficiency. In some embodiments, the donormolecule may be, e.g., another fluorophore, e.g., a quantum dot. Quantumdots, e.g., semiconductor quantum dots are known in the art and aredescribed in, e.g., International Patent Publication No. WO 03/003015.Means of coupling quantum dots to, e.g., biomolecules are known in theart, as reviewed in, e.g., Mednitz et al., NATURE MATERIALS 4:235-46(2005) and U.S. Patent Publication Nos. 2006/0068506 and 2008/0087843,published Mar. 30, 2006, and Apr. 17, 2008, respectively. In someembodiments, quantum dots may be conjugated to a DNA polymerasemolecule. As already discussed above for conjugating enzymes to linkersites, the skilled artisan will undoubtedly appreciate that whenconjugating fluorophores to, e.g., a DNA polymerase or ligase, care mustbe taken to retain enzyme function by mitigating any effect ofconjugating the fluorophore on the primary, secondary, and tertiarystructures of the enzyme.

(b) Multi-Photon Excitation

In some embodiments, a chromophore may be excited by two or morephotons. For example, in some embodiments, excitation of either a donoror acceptor chromophore in FRET may be via two or more photons.Two-photon and multi-photon excitation are described further in, e.g.,U.S. Pat. Nos. 6,344,653 and 5,034,613.

(c) Time-Resolved Detection

In some embodiments, the excitation light source and light detectors ofa detection system may be modulated to have a characteristic phaseshift. Using methods known in the art, for example, as disclosed in U.S.Patent Publication No. 2008/0037008, published Feb. 14, 2008, lightemitted from a molecule being detected on the detection system may bemeasured by a corresponding light detector without interference from anexcitation light source.

(d) Other Fluorescent Detection Systems and Methods

In some embodiments, methods relate to detection of light emitted by atleast one object in a biological cell, which can be a living or fixedcell. In some embodiments, the at least one object is chosen from atleast one object comprising at least one quantum dot, at least oneobject comprising at least one fluorescent protein, and at least oneobject comprising at least one fluorescent small chemical moiety. Insome embodiments, the at least one object is fluorescently labeled andcomprises at least one oligonucleotide, polynucleotide, oligopeptide,polypeptide, oligosaccharide, polysaccharide, or lipid.

In some embodiments, the at least one object comprises a fixed andlimited number of fluorophores, such as at most 20, 10, 5, or 2fluorophores, which can be chosen from quantum dots, fluorescentproteins, and fluorescent small chemical moieties. In some embodiments,the at least one object comprises only a single fluorophore chosen froma quantum dot, a fluorescent protein, and a fluorescent small chemicalmoiety. Many examples of fluorescent small chemical moieties arediscussed above. In some embodiments, fluorescent small chemicalmoieties have an emission peak between 300 and 800 nm and/or a quantumyield (fraction of photons emitted per photon of peak absorptionwavelength absorbed) of at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,or 0.9.

3. EXAMPLES 3.1 Example 1 Preparation of a Nano-Sphere Light Couplerwith a Nucleic Acid-Synthesizing Reaction Complex Localized on itsSurface

A single-stranded circular DNA template is constructed using the processschematized in FIG. 8. A pool of target double-stranded nucleic acidfragments is denatured and combined with self-complementary adapternucleic acid molecules. The adapter nucleic acid molecules compriseoverhanging sequences that are complementary to the ends of one strandof each of the target nucleic acid fragments. The adapter molecules areallowed to anneal to the single-stranded target strands, and a ligatingenzyme is added to ligate the adapter molecules to each of the targetnucleic acid fragments. The products of this ligation are then denaturedand combined with a linking nucleic acid molecule that is complementaryto both adapter molecule sequences ligated to the ends of each targetstrand. Each target strand is then circularized using a ligating enzyme.

The circularized target strand and hybridized linking nucleic acidmolecule are combined with a DNA polymerase, dNTPs, and appropriatebuffer components to form a nucleic acid-synthesizing reaction complex,where the linking nucleic acid molecule functions as a sequencingprimer. The target strand is then replicated in a continuous manner,wherein the polymerase proceeds around the circular template repeatedly,displacing the nascent strand from the template in successivereplications of the template. This produces a nascent strand of DNAcontaining multiple copies of the complement of the target sequence,where each of these copies is separated by a segment having the sequenceof the sequencing primer.

The surface of a nano-sphere particle is chemically modified withstreptavidin. Biotinylated oligonucleotide primers comprising a sequencecomplementary to the sequence of the sequencing primer (the linkingnucleic acid molecule) are combined with the streptavidin-modifiednano-sphere, thereby linking the biotinylated primers to thenano-sphere. The oligonucleotide-coated nano-sphere is combined with thereaction complex comprising the DNA polymerase, circular templatestrand, and replicated strand described in the preceeding paragraph. Thesequencing primer sequences embedded in the replicated strand hybridizeto the oligonucleotides immobilized on the surface of the nano-sphere,thereby anchoring the reaction complex to the surface of the nano-sphereas illustrated in FIG. 9.

3.2 Example 2 Preparation of a Nano-Sphere Light Coupler with a NucleicAcid-Synthesizing Reaction Complex Localized on One Hemisphere UsingSpecific Primers

A nano-sphere particle is modified on one hemisphere with streptavidin.Biotinylated oligonucleotide primers each comprising a sequencecomplementary to the sequence of a sequencing primer (e.g., a linkingnucleic acid molecule as shown in FIG. 8) are combined with thestreptavidin-modified nano-sphere, thereby linking the biotinylatedprimers to the streptavidin-coated hemisphere of the nano-sphere. Theoligonucleotide-coated nano-sphere is combined with a reaction complexcomprising a DNA polymerase, circular template strand, and replicatedstrand as described in Example 1. The sequencing primer sequencesembedded in the replicated strand hybridize to the complementaryoligonucleotides immobilized on one hemisphere of the nano-sphere,thereby anchoring the reaction complex to the surface of the nano-sphereas illustrated in FIG. 10.

3.3 Example 3 Preparation of a Nano-Sphere Light Coupler with a NucleicAcid-Synthesizing Reaction Complex Localized on One Hemisphere UsingRandom-Sequence Primers

A nano-sphere is modified on one hemisphere with streptavidin.Biotinylated oligonucleotide primers each comprising a random nucleotidesequence are combined with the streptavidin-modified nano-sphere,thereby linking the biotinylated primers to the streptavidin-coatedhemisphere of the nano-sphere. The oligonucleotide-coated nano-sphere iscombined with a reaction complex comprising a DNA polymerase, circulartemplate strand, and replicated strand as described in Example 1. Thenascent replicated strand hybridizes to the oligonucleotides immobilizedon one hemisphere of the nano-sphere, thereby anchoring the reactioncomplex to the surface of the nano-sphere as illustrated in FIG. 11.

3.4 Example 4 Preparation of a Nano-Sphere Light Coupler with a NucleicAcid-Synthesizing Reaction Complex Localized on One Hemisphere by aBiotinylated, Double-Stranded Template

A double-stranded circular DNA template is constructed using the processschematized in FIG. 12. A pool of target double-stranded nucleic acidfragments is denatured and combined with self-complementary adapternucleic acid molecules. The adapter nucleic acid molecules compriseoverhanging sequences that are complementary to the ends of one strandof each of the target nucleic acid fragments. The adapter molecules areallowed to anneal to each single-stranded target strand, and a ligatingenzyme is added to ligate the adapter molecules to each target nucleicacid fragment. The products of this ligation are then denatured andcombined with a linking nucleic acid molecule that is complementary toboth adapter molecule sequences ligated to the ends of each targetstrand. Each target strand is then circularized using a ligating enzyme.

A nucleic acid polymerase and a dNTP mixture supplemented withbiotin-dUTP are added to the annealed DNA molecules. The hybridizedlinking nucleic acid molecule functions as a sequencing primer, and asecond strand comprising biotinylated uracil bases is synthesized usinga polymerase without strand-displacing activity. A ligating enzymeincluded in the synthesis mixture forms a closed, circular,double-stranded DNA when the polymerase completes synthesis of thesecond strand.

The closed, circular, double-stranded DNA is denatured and mixed with anano-scale particle with one hemisphere modified with streptavidin. TheDNA and streptavidin-modified particle are combined at an appropriatemolar ratio for a single template to be attached per nano-sphereparticle, as illustrated in FIG. 13A. The nonbiotinylated strand islocalized on the surface of the nano-sphere by virtue of beingintertwined with the biotinylated strand localized on the surface of thenano-sphere.

DNA polymerase, a sequencing primer complementary to the target strand,fluorescently labeled dNTPs, and appropriate buffer components arecombined with the nano-sphere and bound template, allowing aDNA-synthesizing reaction complex to form on the surface of thenano-sphere (FIG. 13B). The polymerase proceeds around the template,forming a nascent synthesized strand (FIG. 13C).

3.5 Example 5 Localization at a Waveguide Adapter Site of a MagneticNano-Sphere with a Surface-Localized Nucleic Acid-Synthesizing Complex

A nano-sphere particle is uniformly surface-modified with magneticfunctional groups. A nucleic acid-synthesizing reaction complex islocalized onto the magnetically-modified surface of the nano-sphere asdescribed in Example 1. The nano-sphere with surface-localized reactioncomplex is localized at an adapter site formed in a waveguide by use ofmicro-fabricated coils located underneath the adapter site. Passing anelectric current through the micro-fabricated coils generates a magneticfield which traps the nano-sphere with surface-localized reactioncomplex at the adapter site. Thus, the reaction complex is localized onthe surface of a light coupler at an adapter site in the waveguide, andmay be localized in the confined space near the surface of the corelayer of the waveguide.

3.6 Example 6 Localization at a Waveguide Adapter Site of anAsymmetrically Magnetic Nano-Sphere with a Surface-Localized NucleicAcid-Synthesizing Complex

A nano-sphere particle is modified with magnetic functional groups on aportion of its surface. A nucleic acid-synthesizing reaction complex islocalized onto the magnetically-modified surface of the nano-sphere asdescribed in any one of Examples 2-4, wherein the same surface of thenano-sphere that is modified with magnetic functional groups is alsomodified with streptavidin. The nano-sphere with surface-localizedreaction complex is localized at an adapter site formed in a waveguideby use of micro-fabricated coils located underneath the adapter site.Passing an electric current through the micro-fabricated coils generatesa magnetic field which traps the nano-sphere with adsorbed reactioncomplex at the adapter site, with the magnetically-modified surface withadsorbed reaction complex facing the core layer of the waveguide. Thus,the reaction complex is localized at the adapter site in the confinedspace near the surface of the core layer of the waveguide.

3.7 Example 7 Localization at a Waveguide Adapter Site of a ConductingMaterial-Modified Nano-Sphere with a Surface-Localized NucleicAcid-Synthesizing Complex

A nano-sphere particle is uniformly surface-modified with conductingmaterial, i.e. material comprising charged groups. A nucleicacid-synthesizing reaction complex is localized on the conductingmaterial-modified surface of the nano-sphere as described in Example 1.The nano-sphere with surface-localized reaction complex is localized atan adapter site formed in a waveguide by use of a micro-fabricatedelectrode at the adapter site. The micro-fabricated electrode comprisesa glass slide located underneath the adapter site, where the glass slideis coated with a layer of conducting material, e.g., indium tin oxide,which acts as the electrode conducting surface. A glass slide that issimilarly coated with a conducting material and that is located abovethe sample solution containing the reaction-complex-loaded nano-spheresacts as the counteracting electrode. Electric current is applied to themicro-fabricated electrodes to generate an electric potential differencebetween the electrodes which traps the nano-sphere withsurface-localized reaction complex at the adapter site. Thus, thereaction complex is localized on the surface of a light coupler at anadapter site in the waveguide, and may be localized in the confinedspace near the surface of the core layer of the waveguide.

3.8 Example 8 Localization at a Waveguide Adapter Site of a Nano-SphereAsymmetrically Modified with Conducting Material and with aSurface-Localized Nucleic Acid-Synthesizing Complex

A nano-sphere particle is modified with conducting material on a portionof its surface. A nucleic acid-synthesizing reaction complex islocalized on the conducting material-modified surface of the nano-sphereas described in any one of Examples 2-4, wherein the same surface of thenano-sphere that is modified with conducting material is also modifiedwith streptavidin. The nano-sphere with surface-localized reactioncomplex is localized at an adapter site formed in a waveguide by use ofa micro-fabricated electrode at the adapter site. The micro-fabricatedelectrode comprises a glass slide located underneath the adapter site,where the glass slide is coated with a layer of conducting material,e.g., indium tin oxide, which acts as the electrode conducting surface.A glass slide that is similarly coated with a conducting material andthat is located above the sample solution containing thereaction-complex-loaded nano-spheres acts as the counteractingelectrode. Electric current is applied to the micro-fabricatedelectrodes to generate an electric potential difference between theelectrodes which traps the nano-sphere with surface-localized reactioncomplex at the adapter site, with the surface of the nano-spheremodified with conducting material and the reaction complex facing thecore layer of the waveguide. Thus, the reaction complex is localized atthe adapter site in the confined space near the surface of the corelayer of the waveguide.

3.9 Example 9 Localization at a Waveguide Adapter Site of a HydrophilicGroup-Modified Nano-Sphere with a Surface-Localized NucleicAcid-Synthesizing Complex

A nano-sphere particle is modified with hydrophilic functional groups onone hemisphere and hydrophobic groups on its other hemisphere. A nucleicacid-synthesizing reaction complex is localized on the hydrophilicsurface of the nano-sphere as described in any one of Examples 2-4,wherein the same surface of the nano-sphere that is modified withhydrophilic groups is also modified with streptavidin. The nano-spherewith surface-localized reaction complex is localized at an adapter sitewhich has hydrophilic surface modification at the reaction site and hashydrophobic surface modification outside the reaction site, as shown inFIG. 6 (where surfaces 1 and 3 are hydrophilic, and surfaces 2 and 4 arehydrophobic). The nano-sphere orients at the adapter site with thehydrophilic surface of the nano-sphere having the localized reactioncomplex positioned at the reaction site, facing the core layer of thewaveguide. Thus, the reaction complex is localized at the adapter sitein the confined space near the surface of the core layer of thewaveguide.

3.10 Example 10 Sequencing of a Nucleic Acid-Synthesizing ReactionComplex Localized on a Movable Light Coupler

A nucleic acid-synthesizing reaction complex localized on a nano-sphereparticle is localized at an adapter site formed in a waveguide asdescribed in any one of Examples 5-9. The sample solution comprisesdNTPs labeled at their beta or gamma phosphates with a uniquefluorophore for each of dATP, dCTP, dGTP, and dTTP. The sample solutionmay be supplemented with additional sequencing reagents, such as DNApolymerase and appropriate buffer components. The distance between theDNA replication fork and the surface of the nano-sphere is in the rangeof tens to hundreds of nanometers. At each step of the synthesisreaction, one of the four types of labeled dNTPs associates with theactive site of the reaction complex, where it base pairs with thecorresponding base of the target nucleic acid. The fluorescent label isexcited by the evanescent light field formed at the bottom of adaptersite and/or by the evanescent light field radiating from the surface ofthe nano-sphere. Incorporation of a fluorophore-labeled nucleotidepolyphosphate into the growing nucleotide strand at the active site isdetected in real-time by detecting emission of the dNTP-linkedfluorophore. The identity of each incorporated nucleotide is determinedby its fluorescent label, wherein the fluorescence label is then cleavedfrom the nucleotide upon incorporation into the growing strand. Thesequence of the target nucleic acid is derived by converting thesequence of the fluorescence emission signals detected during thepolymerization reaction into a nucleic acid sequence.

3.11 Example 11 Simulation of the Excitation Light Field GeneratedAround the Surface of a 350 Nm-Diameter Nano-Sphere Light Coupler byOptical Coupling of Light to the Nano-Sphere

A simulation of excitation light propagation through a single modewaveguide comprising an adapter site and a nano-sphere light couplerdemonstrates that a nano-sphere may couple light from the single modewaveguide. Schematic illustrations of a simulated detection systemcomprising a single mode waveguide, comprising a movable light coupleradapter site, and a nano-sphere light coupler are provided in FIG. 14.In the simulated system, both the light coupler nano-sphere (Ta₂O₅) andwaveguide core layer (Ta₂O₅) have a refractive index of 2.26. Thethickness of a core layer of the single mode waveguide is 100 nm, andthe thickness of a lower cladding layer is 500 nm. The cladding layersof the waveguide are composed of SiO₂, having a refractive index of1.487. The movable light coupler nano-sphere has a diameter of 350 nmand is positioned at the adapter site. The adapter site is an inverted,cone-shaped nanowell, and the nanowell has an opening angle (i.e., theangle from one side of the cone to the side directly opposite) of112.6°. The diameter of the circular bottom of the nanowell is 100 nm,and the nanowell is filled with water, which has a refractive index of1.33. In such a configuration, both the light coupler and the core layerallow the propagation of light waves with single transverse electric(TE) and transverse magnetic (TM) modes.

The wavelength of incident light is 473 nm. The stationary electricfield and magnetic field distribution in the system are calculated usingsource-free Maxwell's equations. (See, for reference, Katrin Schmitt andChristian Hoffmann, “High-Refractive-Index Waveguide Platforms forChemical and Biosensing”, in OPTICAL GUIDED-WAVE CHEMICAL AND BIOSENSORSI, SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 7, 21 (M. Zouroband A. Lakhtakia eds., 2009.))

In this configuration, both the TE-mode and TM-mode fields propagatealong the core layer of the waveguide and the region of the surface ofthe nano-sphere, as shown in FIG. 15 (TE-mode field) and FIG. 16(TM-mode field). Like the stationary electric field, a portion of thestationary magnetic field transfers from the core layer to the region ofthe surface of the nano-sphere, as shown in FIG. 17.

In further simulations, the adapter site is extended into the core layerof the waveguide. The light field of the system wherein the nanowelldoes not extend into the core layer, extends partially into the corelayer, and extends completely into the core layer is shown topologicallyin FIGS. 18 A, B, and C, respectively. The images on the left of FIGS.18 A, B, and C (labeled (a)) depict the intensity contours of the lightfield in the waveguide. The images on the right of FIGS. 18 A, B, and C(labeled (b)) depict the intensity contours of the light field in thedetection system when the nano-sphere is positioned at the adapter site.The energy is transmitted around the waveguide in three kinds ofthickness in the absence of the nano-sphere. However, when thenano-sphere is positioned at the adapter site, a light field will beinduced on the surface of the nano-sphere. The intensity of this inducedlight field increases as the distance which the adapter site extendsinto the core layer of the waveguide increases.

3.12 Example 12 Simulation of the Excitation Light Field GeneratedAround the Surface of a 100 Nm-Diameter Nano-Sphere Light Coupler byOptically Coupling Light to the Nano-Sphere

In a simulation similar to that described in Example 11, the diameter ofa Ta₂O₅ light coupler nano-sphere is 100 nm. The thickness of a Ta₂O₅core layer of the single mode waveguide is 100 nm. The cladding layersof the waveguide are composed of SiO₂. The thickness of a lower claddinglayer is 500 nanometers. The adapter site is a cone-shaped nanowell, andthe opening angle of the conical nanowell (i.e., the angle from one sideof the cone to the side directly opposite) is 112.6°. The diameter ofthe circular bottom of the nanowell is 100 nm, and the nanowell isfilled with water (having a refractive index of 1.33). A schematicillustration of a simulated detection system according to thisconfiguration is provided in FIG. 19. The incident wave is a 473nm-wavelength TE-polarized optical field. The majority of the electricfield remains in the immediate proximity to the core layer of thewaveguide, as shown in FIG. 20(a; right image), which provides a contourmap of the simulated stationary electric field distribution. The lightenergy of the detection system is shown in FIG. 20(b), which illustratesthe light field induced on the lower surface of the nano-sphere (shownat high magnification at right).

In a further simulation, the system diagrammed in FIG. 19 is utilized,but the thickness of the core layer of the waveguide is 50 nm instead of100 nm. The incident wave is a 473 nm-wavelength TE-polarized opticalfield. The simulated stationary electric field distribution is shown inFIG. 21. The light field induced on the lower surface of the nano-sphereis shown in the lower images of FIG. 21.

In a further simulation, the system diagrammed in FIG. 19 is utilized,but the thickness of the core layer of the waveguide is 150 nm insteadof 100 nm. The incident wave is a 473 nm-wavelength TE-polarized opticalfield. The simulated stationary electric field distribution is shown inFIG. 22. The light field induced on the lower surface of the nano-sphereis shown in the lower images of FIG. 22.

In these configurations, a portion of the stationary electric field andthe light energy transfers from the core layer of the waveguide to thelower region of the surface of the nano-sphere, as shown in FIGS. 20, 21and 22.

What is claimed is:
 1. A single-molecule detection system, comprising: amovable light coupler; a waveguide comprising: a core layer, a firstcladding layer formed on the core layer, and a second cladding layerformed below the core layer, wherein at least one adapter site for themovable light coupler is formed in the first cladding layer withoutextending into the core layer and the second cladding layer; and a lightdetector; wherein the movable light coupler is able to localize asingle-molecule object at the at least one adapter site, positionableadjacent the core layer, within an evanescent field generated by a lightwave propagating along the core layer, wherein the movable light coupleris configured to couple the evanescent field when the movable lightcoupler is positioned within the evanescent field, thereby allowingformation of an induced light field around the surface of the lightcoupler, wherein the refractive index of the movable light coupler ishigher than the refractive index of the first cladding layer, and therefractive index of the core layer is higher than the refractive indicesof the first cladding layer and the second cladding layer, and whereinthe single-molecule object is not linked to the surface of thewaveguide.
 2. The detection system of claim 1, further comprising alight source.
 3. The detection system of claim 1, wherein the at leastone adapter site for the movable light coupler is a nanowell.
 4. Thedetection system of claim 1, wherein the movable light coupler is anano-scale particle.
 5. The detection system of claim 4, wherein thenano-scale particle has a length of from about 1/10 to twice thewavelength of a light wave propagating along the core layer.
 6. Thedetection system of claim 1, wherein the at least one adapter siteextends through the full thickness of the first cladding layer.
 7. Thedetection apparatus of claim 1, wherein the core layer is made from amaterial selected from at least one of Si_(x)Ti_(1-x)O₂, TiO₂, Ta₂O₅,Nb₂O₅, HfO₂, Al₂O₃, ZrO₂, ZnS, SiN_(x), AlN_(x), TiN_(x), PC, PMMA, OrSu8.
 8. The detection apparatus of claim 1, wherein the movable lightcoupler is made from a material selected from an oxide, a polymer, ametal, a sulfide, a selenide, or a nitride.
 9. The detection apparatusof claim 1, wherein the movable light coupler is made from an oxide. 10.The detection apparatus of claim 9, wherein the oxide is selected fromSiO₂, TiO₂, Ta₂O₅, or Fe₃O₄.
 11. The detection apparatus of claim 8,wherein the movable light coupler is made from a polymer.
 12. Thedetection apparatus of claim 11, wherein the movable light coupler ismade from polystyrene.
 13. The detection apparatus of claim 1, whereinthe movable light coupler has a core-shell structure, comprising a corematerial and a shell material.
 14. The detection apparatus of claim 13,wherein the core material and shell material are different and are eachindependently selected from an oxide, a polymer, a metal, a sulfide, aselenide, or a nitride.
 15. The detection apparatus of claim 1, whereinthe movable light coupler is able to carry a target molecule on at leasta portion of its surface which is adjacent to the core layer in theadapter site.
 16. The detection apparatus of claim 15, wherein themovable light coupler has a property by which the light coupler can belocated at the adapter site in a specific orientation.
 17. The detectionsystem of claim 16, wherein the movable light coupler is a magneticparticle.
 18. The detection apparatus of claim 15, wherein one or moreregions of the surface of the movable light coupler are modified. 19.The detection apparatus of claim 18, wherein one region of the surfaceof the movable light coupler is modified.
 20. The detection apparatus ofclaim 19, wherein the modified region of the surface of the movablelight coupler is from about 10 to 90% of the surface of the movablelight coupler.
 21. The detection apparatus of claim 18, wherein tworegions of the surface of the movable light coupler are modified. 22.The detection apparatus of claim 18, wherein the modification compriseschemical modification.
 23. The detection apparatus of claim 22, whereinthe chemical modification is modification with a functional groupselected from a hydrophobic group or a hydrophilic group.
 24. Thedetection apparatus of claim 22, wherein the Chemical modification ismodification with a hydrophilic group, wherein the hydrophilic group isa charged group.
 25. The detection apparatus of claim 22, wherein thechemical modification is modification with a ligand-coordinating group.26. The detection apparatus of claim 22, wherein the chemicalmodification is a coating with a polymer.
 27. The detection apparatus ofclaim 22, wherein the chemical modification is modification with amagnetic material.
 28. The detection apparatus of claim 18, wherein themovable light coupler comprises a region of surface modification thathas an affinity for the adapter site.
 29. The detection apparatus ofclaim 18, wherein the movable light coupler comprises a region ofsurface modification that is repelled by the adapter site.
 30. Thedetection system of claim 18, wherein the movable light coupler ismodified with an oligonucleotide.
 31. A method of detecting asingle-molecule object, comprising: introducing an incident light from alight source into a waveguide, thereby forming an excitation light inthe waveguide; localizing a single-molecule object on a movable lightcoupler; localizing the movable light coupler at an adapter site formovable light coupler formed in the waveguide, without linking thesingle-molecule object to the surface of the waveguide, the waveguideincluding a first cladding layer, a core layer formed below the firstcladding layer, and a second cladding layer formed below the core layer,and the adapter site being formed in the first cladding layer withoutextending into the core layer and the second cladding layer; exciting,by the excitation light, the single-molecule object localized on themovable light coupler, causing the single-molecule object to emit alight to be detected by a light detector; generating an evanescent fieldintroduced by a light wave propagating along the core layer; andcoupling the evanescent field to the movable light coupler, and therebyallowing formation of induced light field around the surface of thelight coupler, wherein the refractive index of the movable light coupleris higher than the refractive index of the first cladding layer, and therefractive index of the core layer is higher than the refractive indicesof the first cladding layer and the second cladding layer.
 32. A methodof detecting a single-molecule object, comprising: providing a detectionapparatus comprising i) a movable light coupler; ii) a waveguidecomprising: a core layer, a first cladding layer formed on the corelayer, and a second cladding layer formed below the core layer, whereinat least one adapter site for the movable light coupler is formed in thefirst cladding layer without extending into the core layer and thesecond cladding layer; and a light detector; providing at least onebinding moiety capable of binding a single-molecule object; localizingthe at least one binding moiety individually on the movable lightcoupler; providing a single-molecule object molecule to the at least onebinding moiety localized on the movable light coupler; localizing at theadapter site the movable light coupler on which the at least one bindingmoiety and single-molecule object are localized, without linking thesingle-molecule object to the surface of the waveguide; introducing anincident light from a light source into the waveguide, thereby formingan excitation light in the waveguide; exciting, by the excitation light,the single-molecule object molecule bound to the at least one bindingmoiety localized on the movable light coupler, causing thesingle-molecule object to emit a light to be detected by a lightdetector; generating an evanescent field induced by a light wavepropagating along the core layer at the adapter site; and coupling theevanescent field to the movable light coupler, and thereby allowingformation of an induced light field around the surface of the lightcoupler, wherein the refractive index of the movable light coupler ishigher than a refractive index of the first cladding layer, and therefractive index of the core layer is higher than the refractive indicesof the first cladding layer and the second cladding layer.
 33. Thedetection system of claim 1, wherein the refractive index of the movablelight coupler is lower than the refractive index of the core layer. 34.The detection system of claim 1, wherein the refractive index of themovable light coupler approximately equals the refractive index of thecore layer.
 35. The detection system of claim 3, wherein the nanowellhas a cone shape.
 36. The detection system of claim 3, wherein an angleof a sidewall of the nanowell relative to a direction perpendicular to abottom of the nanowell is less than about 60 degree.
 37. The detectionsystem of claim 1, wherein the first cladding layer is made form amaterial including at least one of silicon oxide, magnesium fluoride,calcium fluoride, aluminum oxide, Su8, PMMA, or polycarbonate.